Jaager

I checked the Minwax web site to see if your product was also a dye  and they are fairly explicit in stating that their pre-stain step is important.  They also write to "Test  Test  Test".
Because of the uneven result and it being more extreme where glue was used - this points to this product being a combination of a stain and a dye.
In your situation sort of the worst of both worlds.
A dye is a solution of pigment molecules in water or alcohol. When done, it lives inside the wood and not on the surface.
Back to the beginning, the planks could have been dye treated before they were assembled on the model.  They would have bonded using PVA as if they were bare wood.  If you had done this and if the result was satisfactory - you would be golden.
As Roger wrote, a stain is a type of paint.  It is a suspension of dye particles and when complete = a surface critter.  Not compatible with PVA bonding - because the pores and surface irregularities it needs for attachment are sealed over by the paint.  If the product that you used was strictly a stain - it would probably not be any more uneven than if you had used a paint.  Most paints work better if the surface is first given a primer coat of half strength shellac.  Your hull would probably be OK if you had done this instead of the Minwax primer.
The verb: to stain  describes what both a dye and a translucent paint does.  The noun: stain should refer to to the translucent paint only,  But it obviously does not.  Popular use confuses them and it appears that commercial products also do this.
 
To keep the work reasonable, you can probably treat the inside with shellac that is diluted 1:1 with shellac thinner (ethanol).  Scotch Brite it a bit - carefully so as not to round the wood edges - and either paint it or give it coat of full strength shellac and then paint it.
 
If you are wed to a raw wood look inside, the kit is economical enough that you can buy another one and be more careful with it. 

You could give any of the Rattlesnake kits a pass.  The S.I. has 3 sheets of plans - $35 total - the plans are about as complete as you are likely to get - outside of a monograph - in which  the details for more than what the plans for this ship provides are likely just speculation by the author of the monograph.   There are plans for a few ships in the NMM which have several sheets instead of one.  These ships are usually class leads and the additional sheets are individual decks.  The sort of details there are more like motel layouts than structural component details. 
Even if you lack power tools, you can easily replicate what a current mass market kit provides for a spine and molds using the S.I plans and a good quality fret saw.  Thicker plywood can used and you can make sure at HD or Lowes or local building supply that the plywood sheets are dead flat.  With a bit of simple lofting - the number of molds can be doubled or more and a single layer of planking used.  A good quality wood species be used to do it.

I checked the Minwax web site to see if your product was also a dye  and they are fairly explicit in stating that their pre-stain step is important.  They also write to "Test  Test  Test".
Because of the uneven result and it being more extreme where glue was used - this points to this product being a combination of a stain and a dye.
In your situation sort of the worst of both worlds.
A dye is a solution of pigment molecules in water or alcohol. When done, it lives inside the wood and not on the surface.
Back to the beginning, the planks could have been dye treated before they were assembled on the model.  They would have bonded using PVA as if they were bare wood.  If you had done this and if the result was satisfactory - you would be golden.
As Roger wrote, a stain is a type of paint.  It is a suspension of dye particles and when complete = a surface critter.  Not compatible with PVA bonding - because the pores and surface irregularities it needs for attachment are sealed over by the paint.  If the product that you used was strictly a stain - it would probably not be any more uneven than if you had used a paint.  Most paints work better if the surface is first given a primer coat of half strength shellac.  Your hull would probably be OK if you had done this instead of the Minwax primer.
The verb: to stain  describes what both a dye and a translucent paint does.  The noun: stain should refer to to the translucent paint only,  But it obviously does not.  Popular use confuses them and it appears that commercial products also do this.
 
To keep the work reasonable, you can probably treat the inside with shellac that is diluted 1:1 with shellac thinner (ethanol).  Scotch Brite it a bit - carefully so as not to round the wood edges - and either paint it or give it coat of full strength shellac and then paint it.
 
If you are wed to a raw wood look inside, the kit is economical enough that you can buy another one and be more careful with it. 

I checked the Minwax web site to see if your product was also a dye  and they are fairly explicit in stating that their pre-stain step is important.  They also write to "Test  Test  Test".
Because of the uneven result and it being more extreme where glue was used - this points to this product being a combination of a stain and a dye.
In your situation sort of the worst of both worlds.
A dye is a solution of pigment molecules in water or alcohol. When done, it lives inside the wood and not on the surface.
Back to the beginning, the planks could have been dye treated before they were assembled on the model.  They would have bonded using PVA as if they were bare wood.  If you had done this and if the result was satisfactory - you would be golden.
As Roger wrote, a stain is a type of paint.  It is a suspension of dye particles and when complete = a surface critter.  Not compatible with PVA bonding - because the pores and surface irregularities it needs for attachment are sealed over by the paint.  If the product that you used was strictly a stain - it would probably not be any more uneven than if you had used a paint.  Most paints work better if the surface is first given a primer coat of half strength shellac.  Your hull would probably be OK if you had done this instead of the Minwax primer.
The verb: to stain  describes what both a dye and a translucent paint does.  The noun: stain should refer to to the translucent paint only,  But it obviously does not.  Popular use confuses them and it appears that commercial products also do this.
 
To keep the work reasonable, you can probably treat the inside with shellac that is diluted 1:1 with shellac thinner (ethanol).  Scotch Brite it a bit - carefully so as not to round the wood edges - and either paint it or give it coat of full strength shellac and then paint it.
 
If you are wed to a raw wood look inside, the kit is economical enough that you can buy another one and be more careful with it. 

Bashing does seem to be a common term used here when a kit is improved, upgraded, partially scratch built,etc. 
I first saw the term kit bashing in a plastic model magazine.  There it described the combination of two or more kits of wildly different subjects. A plastic brig with DC3 wings and 1960's 5" destroyer gun  and tank tracks sort of thing.  Based on what what kit bashing originally described, using it to describe what is done here on a kit is being a bit hyperbolic.  Especially if the goal is a model that is an exact opposite of an anachronism.

You could give any of the Rattlesnake kits a pass.  The S.I. has 3 sheets of plans - $35 total - the plans are about as complete as you are likely to get - outside of a monograph - in which  the details for more than what the plans for this ship provides are likely just speculation by the author of the monograph.   There are plans for a few ships in the NMM which have several sheets instead of one.  These ships are usually class leads and the additional sheets are individual decks.  The sort of details there are more like motel layouts than structural component details. 
Even if you lack power tools, you can easily replicate what a current mass market kit provides for a spine and molds using the S.I plans and a good quality fret saw.  Thicker plywood can used and you can make sure at HD or Lowes or local building supply that the plywood sheets are dead flat.  With a bit of simple lofting - the number of molds can be doubled or more and a single layer of planking used.  A good quality wood species be used to do it.

Theoretical question:
If a charcoal pencil - a sorta soft (HB or so) - was used for the line - used over a paint layer - would a spit wet Kleenex rub the mark off before the area was painted over?

You could give any of the Rattlesnake kits a pass.  The S.I. has 3 sheets of plans - $35 total - the plans are about as complete as you are likely to get - outside of a monograph - in which  the details for more than what the plans for this ship provides are likely just speculation by the author of the monograph.   There are plans for a few ships in the NMM which have several sheets instead of one.  These ships are usually class leads and the additional sheets are individual decks.  The sort of details there are more like motel layouts than structural component details. 
Even if you lack power tools, you can easily replicate what a current mass market kit provides for a spine and molds using the S.I plans and a good quality fret saw.  Thicker plywood can used and you can make sure at HD or Lowes or local building supply that the plywood sheets are dead flat.  With a bit of simple lofting - the number of molds can be doubled or more and a single layer of planking used.  A good quality wood species be used to do it.

You could give any of the Rattlesnake kits a pass.  The S.I. has 3 sheets of plans - $35 total - the plans are about as complete as you are likely to get - outside of a monograph - in which  the details for more than what the plans for this ship provides are likely just speculation by the author of the monograph.   There are plans for a few ships in the NMM which have several sheets instead of one.  These ships are usually class leads and the additional sheets are individual decks.  The sort of details there are more like motel layouts than structural component details. 
Even if you lack power tools, you can easily replicate what a current mass market kit provides for a spine and molds using the S.I plans and a good quality fret saw.  Thicker plywood can used and you can make sure at HD or Lowes or local building supply that the plywood sheets are dead flat.  With a bit of simple lofting - the number of molds can be doubled or more and a single layer of planking used.  A good quality wood species be used to do it.

Theoretical question:
If a charcoal pencil - a sorta soft (HB or so) - was used for the line - used over a paint layer - would a spit wet Kleenex rub the mark off before the area was painted over?

I used an old Craftsman 16 gal that could have substituted for a 747 jet engine for noise in a closed area.
I bought a Festool Midi when the Craftsman burned out.  It is quiet, not enough to allow music, but I could ditch the ear muffs.  
Two problems though - it says not to have a cyclone trap in-line - which I insist on - and trap or not, it turns itself off after 15 minutes at most.
Bandsaw ripping of framing stock takes longer than 15 minutes.  Doing the thickness sanding on the ripped stock takes much longer.  A hull of any size (with a reserve for mistakes) can need 60 pieces 2" x 2'  planks.  And that always takes me longer than I imagine it will take  before I start.
The Midi was ~$500 - I checked HomeDepot and bought a 14 gal Rigid for  < $100.  It is about as quiet as the Festool, likes the DustDeputy, and says on as long as I can endure a session.   A radio control On/Off - (budget models bad)  - is a help - it lives in a condo, and I have to unplug it when done because neighbor garage door remotes can turn it on. 
The Festool is $500 that I will never get back and is now a support for the 5 gal cyclone trap catch drum..
My ideal solution for a shop vac is to have it in a room where I ain't.  Alas, this is not an option in a condo.

I used an old Craftsman 16 gal that could have substituted for a 747 jet engine for noise in a closed area.
I bought a Festool Midi when the Craftsman burned out.  It is quiet, not enough to allow music, but I could ditch the ear muffs.  
Two problems though - it says not to have a cyclone trap in-line - which I insist on - and trap or not, it turns itself off after 15 minutes at most.
Bandsaw ripping of framing stock takes longer than 15 minutes.  Doing the thickness sanding on the ripped stock takes much longer.  A hull of any size (with a reserve for mistakes) can need 60 pieces 2" x 2'  planks.  And that always takes me longer than I imagine it will take  before I start.
The Midi was ~$500 - I checked HomeDepot and bought a 14 gal Rigid for  < $100.  It is about as quiet as the Festool, likes the DustDeputy, and says on as long as I can endure a session.   A radio control On/Off - (budget models bad)  - is a help - it lives in a condo, and I have to unplug it when done because neighbor garage door remotes can turn it on. 
The Festool is $500 that I will never get back and is now a support for the 5 gal cyclone trap catch drum..
My ideal solution for a shop vac is to have it in a room where I ain't.  Alas, this is not an option in a condo.

I used an old Craftsman 16 gal that could have substituted for a 747 jet engine for noise in a closed area.
I bought a Festool Midi when the Craftsman burned out.  It is quiet, not enough to allow music, but I could ditch the ear muffs.  
Two problems though - it says not to have a cyclone trap in-line - which I insist on - and trap or not, it turns itself off after 15 minutes at most.
Bandsaw ripping of framing stock takes longer than 15 minutes.  Doing the thickness sanding on the ripped stock takes much longer.  A hull of any size (with a reserve for mistakes) can need 60 pieces 2" x 2'  planks.  And that always takes me longer than I imagine it will take  before I start.
The Midi was ~$500 - I checked HomeDepot and bought a 14 gal Rigid for  < $100.  It is about as quiet as the Festool, likes the DustDeputy, and says on as long as I can endure a session.   A radio control On/Off - (budget models bad)  - is a help - it lives in a condo, and I have to unplug it when done because neighbor garage door remotes can turn it on. 
The Festool is $500 that I will never get back and is now a support for the 5 gal cyclone trap catch drum..
My ideal solution for a shop vac is to have it in a room where I ain't.  Alas, this is not an option in a condo.

Allan,
If I am reading it correctly, what you are doing is lofting new mould shapes at the positions that you have selected.  It is more work, but it would still exactly replicate the hull.
The English seemed to go to laborious means to get their frame sides to define the sides of their gun ports.  The French and North Americans seem to have just used more material and less space in their upper works and cut the ports into the framing timbers.  I make it a goal to only need to use the existing stations from the Body plan to use as patterns for my frames.  I do not do well at drawing curves and doing something like 200 of them instead of just isolating 20 or so station shapes is weeks if not months quicker.  It is also less prone to me induced artifacts.  This means that on average, I am shaping 2-3-4 bends (4-6-8 frames) and their intervening spaces as a unit.  I fill the spaces with low cost Pine held using double sided tape to make it solid and protect the frame edges.
 
I make everything above the main wale a solid wall - no spaces - I find the actual framing there ugly anyway, so I hide it. 
 
In your place, I would use my method instead of POB.  I would use Yellow Poplar.  (Framing lumber Pine will do - specially if you can get No.1 material. HomeDepot "quality" stuff is No.2) The layer thickness where there would be frames can be any convenient dimension. The sum of the layers needs to be equal to the station interval.  It is way more work, but the thicknesses can be set to frame the gun ports without any later cutting in.  The wood species there can be something more pretty than Yellow Poplar.  I used Rock Elm for Renommee gun port sides - a red close to natural mineral pigment red.  By using pin alignments outside the actual frames, the layers are exact and there is an identical pattern in the identical location on both sides of a stack-  The bevels on both sides have their patterns.  No baseboard needed.  Getting the stacks joined properly requires care.  The result is a solid base for single layer planking.  If you fill the gaps between moulds in POB - My way is probably quicker and if you have the machinery -  a serious scroll saw (I use 1/8" blade on a 9" bendtop bandsaw) and a drum sanding table  and a drill press - the alignment pins need a blue million holes.  It makes for a better looking under the planking hull that is hollow if you want to include any guts.
 

Allan,
I say this about the spacing of moulds on a POB build.  It may be only a slight difference in final shape, but altering the placement of the moulds along the central spine to a different position from those defined by the plans is not a good thing to do. Especially if the reason is to have the moulds be at regular and equal distant intervals. This does change the hull curves.   This ship seems to be singularly unique in that it has four sets of Station intervals.  There are 4 sets of frame thicknesses and space thicknesses.  It is fiercely complicated when compared to similar monographs.   I am saying that by moving the station intervals so that they are equally spaced, just for looks does not do anything important. The moulds should be hidden by the planking and not seen anyway.  I do not see the point for having symmetry there.  But this is my particular OCD.  It seems that even the designer of the plans says that moving the stations and rotating them CCW 1.2 degrees machts nicht anyway.  (For me this injects certain questions about the author.) 
 
The 17th century hulls (most of them. anyway) were developed using three stations.  The main one at the deadflat, one forward  and one aft.  The various profile curves that define where are the arc centers produce the two smaller moulds at an arbitrary position fore and aft chosen by the architect.  But the hull shape can be changed by sliding these outer moulds along the keel.  Move the forward one closer to the bow and the entry is more buff.  Move the after one closer to the stern and the run there is fatter.  (If I understand it correctly, Dutch shipbuilders did this with three bends on the ways, instead of on paper.  The English and French had more politicians involved and less trust in the shipbuilders, so they started with paper/parchment.)  The waterlines, buttock lines, diagonal "proof" lines were to check for unwanted hollows or bulges.  These guys did not have test tanks, laminar flow tests, eddy checks.  They used experience and preconceived  prejudice as their "scientific" tests for proper hull form.  Moving the stations is redesigning the hull shape.
 
All these problems are minor factors.  This ship is special.  It is elegant.  It is about a magnitude above any competitors in beauty. Even if CRI-CRI is using the awful POB method, he seems to be capturing the hull curves so far. 

Language differences aside, that is not a frame.  The usual name is "bulkhead".  It is not really a bulkhead either.  What it actually is = a "mold" or "mould"*.   From my time around microbiology, I prefer mould - even if the site spell checker does not. It also does not like a lot of other words we use, such as "futtock".
 
Imagine doing this at 1:48 as provided in the monograph?  
 
* Old Ben, Ben Lankford was the first the make a point of this back on Clay Feldman's listserver.

As an alternative you could cheat:
Part 204 - chock piece  - seems the extend to the top of part 202B - upper head rail.
I would place the two gammoning slots in 204 - just above the upper head rail.
This would save having to move the LWL or hide the carving.
In real life, if the boatswain, I would probably try to place the gammoning where the carving is and adjust the pattern to include it.

If you included a 1.2 degree drag when the central spine was shaped,the stations will be vertical directly from the plans.
 
With a large solid central spine, a POB fabrication appears to be the method here.  The underlying spine/solid molds structure of POB is so unattractive that it all but demands to be totally hidden.  When it is hidden by planking, the regularity and symmetry of the mold intervals is moot.  Why alter the intervals?
 
Changing the spacing of the station intervals will have a small but significant effect on the hull shape, if the stations in the plans are used as mold patterns.
If you loft new patterns at the new intervals the hull shape will be as designed.
 

If you intend to incline the keel and erect  the frames at 90 degrees, this for POF, and you use an upper brace/  locator to align and support the tops pf the frames, it will help to add a line above the tallest frame as a sirmark/ locator for the frame extensions that is perpendicular to the stations/frames.  That would be at a 1.2 degree angle to the present baseline/keel on the plans.
 
If you are doing this POB (and all indicators point to this as being your intention) - it just means that the central spine has to have the 1.2 degree downward slope aft.
When it comes time to position the depth of the molds on the spine, ..... 
I lofted for POF.  I indicate the location of the decks, port sills, bottom of wales, rails on my frame shapes.  I use the profile to provide these positions.  The only reliable lines that I found  that are on both of the Body plan and the Profile plan at each station that can match them up are L.Fon , L.In1 , ( and I guess, I only needed the two) L.In2 , L.For. 
Where they are at each station is where they are at each station outline.  You will need to get these lines transferred across each mold and make sure they also where they need to be on the central spine if you find them as useful/ necessary as I did.
 
And you should have bopped him upside his head for not having the keel at an incline on the original lines plans in the first place.

I am also attracted to Saint-Philippe.  I have developed my own framing method.  It does not use the individual bend patterns that are in the monograph.  I use the outside shape from the Body plan only.  I have lofted S.Philippe for my method.  I have actually plowed this furrow, at least in part, three times.  ( I like the distinctive pattern of the English 17th century Navy Board models. It only uses five timbers per bend. The overlap requires very long timbers with each having much curvature. My scale is 1:60 and an exact replication would require stock that is wider than I wish and too much loss to waste.  I have found another way to get there, but it required at lot of repeat lofting to work out.)  This is a long way of getting to some problems that I have had with the lines plans as presented. 
 
I am going to list those problems - they were written in a recent post but are a bit edited here:
 
 Saint-Philippe is complicated.   The frames and stations are canted forward 1.2 degrees in the Profile Plan.  None of the usual baseline, keel, waterlines,etc. are any help in matching the stations from the profile to the frame outlines (to locate the position of the decks and wales and ports).  It dawned on me that the L.Fon and L.In1 will locate a station profile to its frame outline (sirmarks).   There is one aspect of SP that is diving me to distraction.  On the Profile plan, the station lines are sloped with the frames.  The Body plan seems to match what they would be at 1.2 degrees.  If they are viewed on the plan baseline, they would have to be compressed because the 1.2 degree line is longer ( hypotenuse of a right triangle). But the Body Plan seems to be the actual frame shape, It is the hypotenuse shape and not a foreshortened perpendicular to the keel parallax view.  As a check, I found that the Body plan at M matches the individual bend shape for M in the extracted frames plan.  It is not squished down. In your post #7, observe that the keel is flat to the baseline and the rabbet is horizontal.   So, if the Body plan is perpendicular to the viewer, but is the actual shape, why is the rabbet not sloped down aft?  To get the stations back up to 90 degrees the keel would have to slope 1.2 degrees aft.  The geometry is confusing me.
 
  It would have been more friendly to have drawn the keel with the slope.  However, Lemineur developed the individual bend patterns for the commonly used POF assembly methods and did not think thru just how much more difficult doing it at a 1.2 degree angle is.  It hurts my head to try to see how to use the routine methods to get a new baseline that gets the frames perpendicular, if you choose to mount the keel at an angle., instead of the frames.  The geometry is maddening. 
 
There is another factor that is unique to S.Philippe.  The stations  are not spaced all the same or a derivative of a common factor.  For every other ship that I have investigated, the stations involve some interval of a common frame sided dimension.  Usually, it is the same R&S, with the number of that factor being 4 or 3 or 2 of them per station interval.  The same thickness of framing stock is used for the whole hull.  The intervals for S.Philippe are in 4 different groupings.  They are 12x12.75", 48x15.4", 24x14.9", 43x 13.9" (Imperial inches). (By the way, this is 127 frames or  63 bends.)  It requires four separate thickness of framing stock and constant attention and awareness to where you are.  The tabled mortise joint within a bend is eccentric, but that is not something that I would replicate and is easily ignored.
 
I will be interested in seeing if any of this causes a problem for you and if so, seeing how you solve them.
 

If you are limited in access to tools and have to use only muscle power then the Lime is your friend.
If you have power tools, for POF you might could consider a harder species of wood -
if light color is your choice - Sycamore Maple, Beech, or Birch.
darker would be Pear - we have opposite economical choices - over here Pear is an exotic, difficult to source, and expensive.
for the eastern half of this continent Black Cherry is an adequate but lower quality substitute for Pear.
 
Lime has about everything going for it- except that it is not nearly as hard as should be wanted.

If you are limited in access to tools and have to use only muscle power then the Lime is your friend.
If you have power tools, for POF you might could consider a harder species of wood -
if light color is your choice - Sycamore Maple, Beech, or Birch.
darker would be Pear - we have opposite economical choices - over here Pear is an exotic, difficult to source, and expensive.
for the eastern half of this continent Black Cherry is an adequate but lower quality substitute for Pear.
 
Lime has about everything going for it- except that it is not nearly as hard as should be wanted.

The NRG has just issued its first PDF only supplement to the NRJ.  It is free if your have joined the Guild.  If not, 1) give a thought to joining or 2) the cost for the supplement is low enough to be worth worth buying.  If nothing else, it gives you a view of what the Journal offers and what the past issue CD's are like.  Anyway, in the supplement is an impressive full page ad for the MS  Model ShipWright beginner series of models.  I have not built them myself, but the feedback from those who have and the overall quality of what MS produces portends that one are all of this series will get you up to speed at a reasonable investment level. 

The NRG has just issued its first PDF only supplement to the NRJ.  It is free if your have joined the Guild.  If not, 1) give a thought to joining or 2) the cost for the supplement is low enough to be worth worth buying.  If nothing else, it gives you a view of what the Journal offers and what the past issue CD's are like.  Anyway, in the supplement is an impressive full page ad for the MS  Model ShipWright beginner series of models.  I have not built them myself, but the feedback from those who have and the overall quality of what MS produces portends that one are all of this series will get you up to speed at a reasonable investment level. 

The NRG has just issued its first PDF only supplement to the NRJ.  It is free if your have joined the Guild.  If not, 1) give a thought to joining or 2) the cost for the supplement is low enough to be worth worth buying.  If nothing else, it gives you a view of what the Journal offers and what the past issue CD's are like.  Anyway, in the supplement is an impressive full page ad for the MS  Model ShipWright beginner series of models.  I have not built them myself, but the feedback from those who have and the overall quality of what MS produces portends that one are all of this series will get you up to speed at a reasonable investment level.