Jaager

Wow, Bruce !!  Boxwood!   logs though - likely not too large-  Unless it is possible to access a band saw 14" or large - processing it will involve frustration and agony - would not consider it for framing but grabbing a serious supply for use as blocks, catheads, davits,  bitts ,  belfreys,  is worth considering.
The Pear though -  if it is quality and is 4x4 or 8x4  and the price is reasonable - back up a truck and fill it.
 
Matrim,
I would score everything on your list as an excellent choice but the Red Cedar.  I have no experience with it.  Beech seems similar to Hard Maple  but a tad darker.  Hard Maple and Black Cherry are my choices for framing.  They are domestic species for me and easy to get.  
Basswood is way too soft and iffy about holding a sharp edge to me.  Lime is the same genus but a bit harder - enough harder, I seriously question.   Yellow Poplar  is similar in hardness, but it works as though it were a lot harder.  It will hold a sharp edge.  The stock that I have gotten is excellent for framing - if you totally plank over it.  The color range in a single board can go from tan to green to a color that looks like creosote treated Pine - ugly brown.  Good looks ain't its thing.
POF uses a lot of wood.  A frigate @ 1:48 - you are looking at maybe 10-20 BF.  More if you cut your frames from stock that is glued into a "U" and cement the frame pattern to it, a lot more.
The volume of wood used for everything but framing is reasonable enough to make using imported species worth considering.
For framing, it makes for a more reasonable budget outlay the use species that are domestic where you live.
 
While good Apple is king,  it is a bear to obtain.   Your Pear - Pyrus communis - steamed (Swiss) or not comes in a close second.  I love Black Cherry, but Pear is better.  The hard species of Maple domestic for you is Sycamore maple, European sycamore   Acer pseudoplatanus.   It is probably close enough in hardness to make not worth paying a premium  for imported Acer saccharum.  
 
Because Underhill praised Sycamore Naple,  but called it Sycamore,  I bought a supply of our Sycamore -  American Plane  Platanus occidentalis .  A more awful species would take work to find. well maybe Siberian Elm or Lombardy Poplar.

Wow, Bruce !!  Boxwood!   logs though - likely not too large-  Unless it is possible to access a band saw 14" or large - processing it will involve frustration and agony - would not consider it for framing but grabbing a serious supply for use as blocks, catheads, davits,  bitts ,  belfreys,  is worth considering.
The Pear though -  if it is quality and is 4x4 or 8x4  and the price is reasonable - back up a truck and fill it.
 
Matrim,
I would score everything on your list as an excellent choice but the Red Cedar.  I have no experience with it.  Beech seems similar to Hard Maple  but a tad darker.  Hard Maple and Black Cherry are my choices for framing.  They are domestic species for me and easy to get.  
Basswood is way too soft and iffy about holding a sharp edge to me.  Lime is the same genus but a bit harder - enough harder, I seriously question.   Yellow Poplar  is similar in hardness, but it works as though it were a lot harder.  It will hold a sharp edge.  The stock that I have gotten is excellent for framing - if you totally plank over it.  The color range in a single board can go from tan to green to a color that looks like creosote treated Pine - ugly brown.  Good looks ain't its thing.
POF uses a lot of wood.  A frigate @ 1:48 - you are looking at maybe 10-20 BF.  More if you cut your frames from stock that is glued into a "U" and cement the frame pattern to it, a lot more.
The volume of wood used for everything but framing is reasonable enough to make using imported species worth considering.
For framing, it makes for a more reasonable budget outlay the use species that are domestic where you live.
 
While good Apple is king,  it is a bear to obtain.   Your Pear - Pyrus communis - steamed (Swiss) or not comes in a close second.  I love Black Cherry, but Pear is better.  The hard species of Maple domestic for you is Sycamore maple, European sycamore   Acer pseudoplatanus.   It is probably close enough in hardness to make not worth paying a premium  for imported Acer saccharum.  
 
Because Underhill praised Sycamore Naple,  but called it Sycamore,  I bought a supply of our Sycamore -  American Plane  Platanus occidentalis .  A more awful species would take work to find. well maybe Siberian Elm or Lombardy Poplar.

If spars are missing, or too damaged to repair, fix that.  Do it in a way that matches.  I totally agree with Bob,  refinishing is not the wise choice.  If this model was ever intended to sail in an actual pond,  it is not probable that shellac was used as a clear finish final coat anywhere on it.  Shellac loves water.  It loves it so much that it grabs it and turns white.  In the 1930's a water proof clear finish would be vanish.  Traditional varnish - boiled linseed oil cooked with shellac in mineral spirits or terp.  Carefully remove any dirt and muck condensed on it from the its environment - look up restoration cleaning methods.  Give it a home that protects it from dust and temporary gaseous goo like tobacco smoke and frying oils.   If something bright and shiny for you to sail is your original goal, I suggest that you leave the old girl in her retirement and build a new one yourself. 

This is not exactly the lay of the land.   My view of it is that there are more than 3 types.  I do not use 2 of the 3 that you have listed.
Contact glue/cement - here Weldwood is the common brand - has zero place on an actual ship model.  I use it to fix sanding media (cloth backed) to the Maple drum of my homemade thickness sander - difficult and messy to remove. 
CA -  do not use it - probably a generational thing - but when I did try it, I never got much use from a bottle before it dried up.  Depending on brand and conditions, if want a model to last a hundred or more years and not just 20 or so,  the long term stability is open to question.  
PVA -  comes four main flavors - white - OK, but I do not favor it,  yellow - carpenter's glue  I use the water resistant Titebond II brand,  brownish - fully water proof = Titebond III (really acidic),  archival white - bookbinders neutral pH - safe for rigging lines made from natural fibers ie. linen or cotton.
Epoxy  -  many types -  the bond for metal to wood
Hide glue - really traditional - not used much -  the liquid variety is in disfavor because of its high water content (probably).  The glue pot type is messy and time consuming.  Fully archival.
 
Before it sets, PVA squeeze out is easy to remove - scrape it or damp paper towel - once set  a very sharp edge - it is a plastic.   Undoing a bond - near 100% isopropyl alcohol  and a heat gun.
 
Are you sure it was not wood that had been dyed?  A wood dye penetrates wood and does not affect its pores or surface.  A stain is really semi transparent paint and it is pointless and bit mad to use PVA on a painted or stained surface.
 
Wood bending?  The tools to do it?  You pays your money and you takes your chances,   Whatever works for you.  The most important factor here is your choice of wood species to try to bend to begin with.  A few bend well,  most sorta do, and some resist bending to a degree that makes it not worth even trying.

This is not exactly the lay of the land.   My view of it is that there are more than 3 types.  I do not use 2 of the 3 that you have listed.
Contact glue/cement - here Weldwood is the common brand - has zero place on an actual ship model.  I use it to fix sanding media (cloth backed) to the Maple drum of my homemade thickness sander - difficult and messy to remove. 
CA -  do not use it - probably a generational thing - but when I did try it, I never got much use from a bottle before it dried up.  Depending on brand and conditions, if want a model to last a hundred or more years and not just 20 or so,  the long term stability is open to question.  
PVA -  comes four main flavors - white - OK, but I do not favor it,  yellow - carpenter's glue  I use the water resistant Titebond II brand,  brownish - fully water proof = Titebond III (really acidic),  archival white - bookbinders neutral pH - safe for rigging lines made from natural fibers ie. linen or cotton.
Epoxy  -  many types -  the bond for metal to wood
Hide glue - really traditional - not used much -  the liquid variety is in disfavor because of its high water content (probably).  The glue pot type is messy and time consuming.  Fully archival.
 
Before it sets, PVA squeeze out is easy to remove - scrape it or damp paper towel - once set  a very sharp edge - it is a plastic.   Undoing a bond - near 100% isopropyl alcohol  and a heat gun.
 
Are you sure it was not wood that had been dyed?  A wood dye penetrates wood and does not affect its pores or surface.  A stain is really semi transparent paint and it is pointless and bit mad to use PVA on a painted or stained surface.
 
Wood bending?  The tools to do it?  You pays your money and you takes your chances,   Whatever works for you.  The most important factor here is your choice of wood species to try to bend to begin with.  A few bend well,  most sorta do, and some resist bending to a degree that makes it not worth even trying.

This is not exactly the lay of the land.   My view of it is that there are more than 3 types.  I do not use 2 of the 3 that you have listed.
Contact glue/cement - here Weldwood is the common brand - has zero place on an actual ship model.  I use it to fix sanding media (cloth backed) to the Maple drum of my homemade thickness sander - difficult and messy to remove. 
CA -  do not use it - probably a generational thing - but when I did try it, I never got much use from a bottle before it dried up.  Depending on brand and conditions, if want a model to last a hundred or more years and not just 20 or so,  the long term stability is open to question.  
PVA -  comes four main flavors - white - OK, but I do not favor it,  yellow - carpenter's glue  I use the water resistant Titebond II brand,  brownish - fully water proof = Titebond III (really acidic),  archival white - bookbinders neutral pH - safe for rigging lines made from natural fibers ie. linen or cotton.
Epoxy  -  many types -  the bond for metal to wood
Hide glue - really traditional - not used much -  the liquid variety is in disfavor because of its high water content (probably).  The glue pot type is messy and time consuming.  Fully archival.
 
Before it sets, PVA squeeze out is easy to remove - scrape it or damp paper towel - once set  a very sharp edge - it is a plastic.   Undoing a bond - near 100% isopropyl alcohol  and a heat gun.
 
Are you sure it was not wood that had been dyed?  A wood dye penetrates wood and does not affect its pores or surface.  A stain is really semi transparent paint and it is pointless and bit mad to use PVA on a painted or stained surface.
 
Wood bending?  The tools to do it?  You pays your money and you takes your chances,   Whatever works for you.  The most important factor here is your choice of wood species to try to bend to begin with.  A few bend well,  most sorta do, and some resist bending to a degree that makes it not worth even trying.

Does resistance soldering work for this sort of work?

Jim,     what is done under the term "kit bashing" here is hardly bashing.   It is far more like kit improvement or kit augmentation.  What it really is = partially scratch building a kit model.  There was a time when this was the primary path towards full on scratch building.
 
It was years ago that I first encountered kit bashing - it was plastic models and it was things like adding P51 wings to the model of a "56 Chevy.   In our world it would be mounting a 5 inch gun turret in the waist of Drake's Revenge and replacing the swivels with M2.  You might think that it could be further bashed by adding a Volvo Penta and a prop,  but that has already been done for real on a replica of a near contemporary of Revenge, the Susan Constant which is over here at Jamestown.

Does resistance soldering work for this sort of work?

Jim,     what is done under the term "kit bashing" here is hardly bashing.   It is far more like kit improvement or kit augmentation.  What it really is = partially scratch building a kit model.  There was a time when this was the primary path towards full on scratch building.
 
It was years ago that I first encountered kit bashing - it was plastic models and it was things like adding P51 wings to the model of a "56 Chevy.   In our world it would be mounting a 5 inch gun turret in the waist of Drake's Revenge and replacing the swivels with M2.  You might think that it could be further bashed by adding a Volvo Penta and a prop,  but that has already been done for real on a replica of a near contemporary of Revenge, the Susan Constant which is over here at Jamestown.

If what you have is Lovoa trichilioides  - what the Wood Database lists as African Walnut,  trying to get a serious bend is fighting against the basic structure of the wood.
The grain is likely interlocked.  This offers resistance to the fiber bundles sliding along side each other to produce a staggered formation.  It might be more productive to substitute with a species that allows bending.  Then spend the additional effort find a mixture of wood dyes that color the substitute to match the Walnut that you have used.

Not a recommendation,  just a comment:
My background is in the Biological Sciences, and HMS Beagle has a role similar to an icon. Beagle had been a will-o'-the-wisp as a subject for a model until 1997.  Then it became my first choice to build after retirement because Karl Heinz Marquardt authored an Anatomy Of The Ship volume covering HMS Beagle.   I scratch build and have been able to loft the framing for this ship, using the information and plans in the book.  I even have the necessary stock of framing wood.  I have long  been diverted from building Beagle.  I have decided to use 1:60 as the scale for all of the ships that I model.  I have a "rule" against modeling a ship that is available as a kit.   Sort of like the on going mission of the Starship Enterprise: "to go where....".  This new OcCre kit - at 1:60 - has provided me with a bit of a dilemma.  Being POF it would not be mistaken for the kit, but still...  OK, enough irrelevant rambling!
The AOTS volume - while possibly difficult to buy - is probably also the basis of the kit.  It also provides information that allows for an extraordinary level of detail - if you so choose.  In addition the information and level of detail for the spars, rigging and sails is extensive and is matched by only a few other vessels.   If the rigging gives you pause, the kit plus the book provides enough information  that an y impediment will be at the level of your effort and not due to a lack of information.

If what you have is Lovoa trichilioides  - what the Wood Database lists as African Walnut,  trying to get a serious bend is fighting against the basic structure of the wood.
The grain is likely interlocked.  This offers resistance to the fiber bundles sliding along side each other to produce a staggered formation.  It might be more productive to substitute with a species that allows bending.  Then spend the additional effort find a mixture of wood dyes that color the substitute to match the Walnut that you have used.

Unless the case has good ventilation, it could turn into an oven.  I think the effect is = visible light passes thru the glass, upon striking a surface inside it loses energy.  The lower energy is IR and it reflects from the glass and bounces around inside or increases the temp of any material that it hits. 
Man made fibers are catalyzed cross linked polymers.  UV can act as a catalyst to produce additional cross linking.  The more cross linking, the more rigid it becomes.  Rigid is brittle, until under any stress, even a change in temp, it shatters.   The location that you have chosen increases the rate at which organic materials follow Nature's imperative to return to CO2 and H2O.

Unless the case has good ventilation, it could turn into an oven.  I think the effect is = visible light passes thru the glass, upon striking a surface inside it loses energy.  The lower energy is IR and it reflects from the glass and bounces around inside or increases the temp of any material that it hits. 
Man made fibers are catalyzed cross linked polymers.  UV can act as a catalyst to produce additional cross linking.  The more cross linking, the more rigid it becomes.  Rigid is brittle, until under any stress, even a change in temp, it shatters.   The location that you have chosen increases the rate at which organic materials follow Nature's imperative to return to CO2 and H2O.

Afonso,
My suggestion was that you build completely from just plans and materials that you directly obtain.  I based this on you being on a mission and seriously focused on it.
I see now that you are coming in to this with less of a view of this landscape than I thought.
Before the internet,  when starting this,  it was a local club - if you were extremely lucky,  otherwise it was books and magazines or journals dedicated to ship modeling and books about building the original ships, some of the books were reprints of books written at the time of the ships.   The best of the books and best of the journal articles demonstrated and encouraged building from scratch.   Unless your previous experience involved woodworking at the cabinet maker or fine furniture maker level,  the learning curve was/is steep.  It pretty much requires owning or having access to some fairly expensive tools, especially at the milling your own stock from lumber stage.  When you have the materials - mainly wood stock with the proper dimensions - expensive tools are not necessary, but they make things go faster and easier.  But you still will not be able to mimic Graham Chapman and build a model in bed, at night in the dark. (Monty Python)
A ship, especially a warship,  involved/involves the most advanced technology of the culture building it.  It is a serious endeavor.  Should you wish to build a model of one, a model that is reasonably close to the original and that, in your imagination, could grace a museum,  building it from scratch is still the way.  This is especially true if your subject is unique or has been rarely modeled.  Kits are primarily about making money for the mfg.  They require being economical with the component materials, using methods that as many as possible can execute, and subjects with broad appeal and are supplied in  large numbers.  At the extreme, it is about selling a fantasy, an expensive fantasy that is more often than not beyond the existing skills of the buyer.  At that level,  the skill involved in the overall process is in the advertising, not in craftsmanship. 

You could maybe buy some wider stock that is the thickness of the planking so that it can be spilled.
Before you segment the planking area,  two planks need to be in place and correct:
The lower wale and the garboard.  For the garboard, only one edge should be spilled and that is the edge that meets the keel.
Mark's lower red line is the garboard and his length is how long it is.  It does not chase the rabbet up the stem.
In the era of your model, I don't think the ends of the wale strakes tapered at the ends.
 
Get some thick hard pressed cardboard  and fully plank with it.  When you get that correct, the pieces can be used as patterns for the wood.
But the more wood strakes are applied, the less reliable will be the cardboard patterns.  But new ones that fit the smaller space would be better.

Afonso,
My suggestion was that you build completely from just plans and materials that you directly obtain.  I based this on you being on a mission and seriously focused on it.
I see now that you are coming in to this with less of a view of this landscape than I thought.
Before the internet,  when starting this,  it was a local club - if you were extremely lucky,  otherwise it was books and magazines or journals dedicated to ship modeling and books about building the original ships, some of the books were reprints of books written at the time of the ships.   The best of the books and best of the journal articles demonstrated and encouraged building from scratch.   Unless your previous experience involved woodworking at the cabinet maker or fine furniture maker level,  the learning curve was/is steep.  It pretty much requires owning or having access to some fairly expensive tools, especially at the milling your own stock from lumber stage.  When you have the materials - mainly wood stock with the proper dimensions - expensive tools are not necessary, but they make things go faster and easier.  But you still will not be able to mimic Graham Chapman and build a model in bed, at night in the dark. (Monty Python)
A ship, especially a warship,  involved/involves the most advanced technology of the culture building it.  It is a serious endeavor.  Should you wish to build a model of one, a model that is reasonably close to the original and that, in your imagination, could grace a museum,  building it from scratch is still the way.  This is especially true if your subject is unique or has been rarely modeled.  Kits are primarily about making money for the mfg.  They require being economical with the component materials, using methods that as many as possible can execute, and subjects with broad appeal and are supplied in  large numbers.  At the extreme, it is about selling a fantasy, an expensive fantasy that is more often than not beyond the existing skills of the buyer.  At that level,  the skill involved in the overall process is in the advertising, not in craftsmanship. 

Afonso,
My suggestion was that you build completely from just plans and materials that you directly obtain.  I based this on you being on a mission and seriously focused on it.
I see now that you are coming in to this with less of a view of this landscape than I thought.
Before the internet,  when starting this,  it was a local club - if you were extremely lucky,  otherwise it was books and magazines or journals dedicated to ship modeling and books about building the original ships, some of the books were reprints of books written at the time of the ships.   The best of the books and best of the journal articles demonstrated and encouraged building from scratch.   Unless your previous experience involved woodworking at the cabinet maker or fine furniture maker level,  the learning curve was/is steep.  It pretty much requires owning or having access to some fairly expensive tools, especially at the milling your own stock from lumber stage.  When you have the materials - mainly wood stock with the proper dimensions - expensive tools are not necessary, but they make things go faster and easier.  But you still will not be able to mimic Graham Chapman and build a model in bed, at night in the dark. (Monty Python)
A ship, especially a warship,  involved/involves the most advanced technology of the culture building it.  It is a serious endeavor.  Should you wish to build a model of one, a model that is reasonably close to the original and that, in your imagination, could grace a museum,  building it from scratch is still the way.  This is especially true if your subject is unique or has been rarely modeled.  Kits are primarily about making money for the mfg.  They require being economical with the component materials, using methods that as many as possible can execute, and subjects with broad appeal and are supplied in  large numbers.  At the extreme, it is about selling a fantasy, an expensive fantasy that is more often than not beyond the existing skills of the buyer.  At that level,  the skill involved in the overall process is in the advertising, not in craftsmanship. 

You could maybe buy some wider stock that is the thickness of the planking so that it can be spilled.
Before you segment the planking area,  two planks need to be in place and correct:
The lower wale and the garboard.  For the garboard, only one edge should be spilled and that is the edge that meets the keel.
Mark's lower red line is the garboard and his length is how long it is.  It does not chase the rabbet up the stem.
In the era of your model, I don't think the ends of the wale strakes tapered at the ends.
 
Get some thick hard pressed cardboard  and fully plank with it.  When you get that correct, the pieces can be used as patterns for the wood.
But the more wood strakes are applied, the less reliable will be the cardboard patterns.  But new ones that fit the smaller space would be better.

Afonso,
First off  - what is your location on Terra?
Second - You have set up a situation with mutually exclusive requirements.  Kit + 16th C.,17th C., + Iberia + accurate
There are a few vessels from that time with documentation.  Vasa is sort of at the top - Northern Europe  . 
Most of the recent finds from your area of interest have been done by nautical archaeologists.  It is my impression that they do not hold us  in high regard.  Little that they find seems to reach us in a form that we can use.
 
Should you change one requirement = kit  to scratch, there are several possibilities. 
This requires that your standards for accurate be realistic.
I have series of books about an Iberian find at Red Bay, Canada,  these plus the recent articles in SIS documenting a model,  could be the basis for a build.
The following will require loose, very loose limits for accuracy:
I have plans for a Manila Galleon - also SIS I think.  This part of SIS is now NRG content?
AOTS has a volume with speculative plans for the first squadron of C.Columbus.  ( also from Britain  Mary Rose and Susan Constant ) 
Wm Baker did plans for Mayflower - with some aspects and choices being seriously questioned.
In the 1970's  there was available from Verlag Delius, Klasing & Co. a series of books with plans for your time of interest. They may appear for sale from time to time.
Osprey has a Spanish Galleon issue.
NIP volume - probably Conway - The Galleon by Peter Kirsch.
There are several books  about Kogg finds.
The maritime museums in Iberia may have plans or plans of reconstructions.
Until your skill level reaches a level where you do not need to ask,  I seriously advise sailing well away from kits or plans for multi deck warships - especially those from the 17th C.

Afonso,
First off  - what is your location on Terra?
Second - You have set up a situation with mutually exclusive requirements.  Kit + 16th C.,17th C., + Iberia + accurate
There are a few vessels from that time with documentation.  Vasa is sort of at the top - Northern Europe  . 
Most of the recent finds from your area of interest have been done by nautical archaeologists.  It is my impression that they do not hold us  in high regard.  Little that they find seems to reach us in a form that we can use.
 
Should you change one requirement = kit  to scratch, there are several possibilities. 
This requires that your standards for accurate be realistic.
I have series of books about an Iberian find at Red Bay, Canada,  these plus the recent articles in SIS documenting a model,  could be the basis for a build.
The following will require loose, very loose limits for accuracy:
I have plans for a Manila Galleon - also SIS I think.  This part of SIS is now NRG content?
AOTS has a volume with speculative plans for the first squadron of C.Columbus.  ( also from Britain  Mary Rose and Susan Constant ) 
Wm Baker did plans for Mayflower - with some aspects and choices being seriously questioned.
In the 1970's  there was available from Verlag Delius, Klasing & Co. a series of books with plans for your time of interest. They may appear for sale from time to time.
Osprey has a Spanish Galleon issue.
NIP volume - probably Conway - The Galleon by Peter Kirsch.
There are several books  about Kogg finds.
The maritime museums in Iberia may have plans or plans of reconstructions.
Until your skill level reaches a level where you do not need to ask,  I seriously advise sailing well away from kits or plans for multi deck warships - especially those from the 17th C.

Mark,
I did not notice until your replacement molds made it obvious,  Belle was a bit of an out layer. The degree of hollow at the bow is more than Sea Witch even and Griffiths was heavily criticized for designing that.  I wonder why Belle did not set a trend?
Dean
 

What may have been going on =
The number of trees that are suited for warship construction is finite,  especially on an island that is not all that large to begin with.  In the zeal the build a large navy, all of the large old growth Oak was cut.  They had to sacrifice their standards to match what they could obtain.   
 
Unless the project is a cross section,  in a model,  it is a detail difficult to see.  A close, but easier technique; have the clamp stop at the bottom of the beam and fit a short piece of the same wood  between the beams that is the depth of the dovetail.  Done well, the glue joint may appear to be wood grain.

Rick,
This may have been Fate handing you a small mercy, and a choice to take a kinder path.  I have a recollection of reading that far more SOS kits may reside at the back of closet selves than ever see completion.  Building the original helped trigger a revolution.  The ship is a first rate liner.  It had more sculptures than a lot of museums.  A sail flagship is a formidable challenge no matter how many models in the experience bank of the model shipwright.   The salesmen weave a fantastic illusion of what you can have on your fireplace mantle,  and try to trigger an impulse buy.   It is not dropping a beginning swimmer into the deep end, it is dropping him into a storm tossed ocean with rip currents and whorl pools.   Consider a project with a higher probability of completion to begin.  Lots of advise here on what may be a good choice.  Then, when you are ready,  given where you are, maybe scratch build a model of Otway Burns' Snap Dragon.  Then, if truly mad, the 74gun USS North Carolina.