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My list is not as thorough but here is how I have tackled it for the few I have fully rigged.
1. Install all eyebolts into the hull before installing guns or anything that may get in the way.  Sometimes I attach a block and run a started line through it to tie it out of the way. Te starting threads allow me to just glue the actual line to the end and carefully pull it through later, only need a few inches (less is better to keep from getting confused)
2. As a general rule, I install all rigging from the center of the ship towards the edges and start at the front and work my way back. this means I am not trying to reach through standing rigging later to try and attach something or I have through through how I am going to reach a center line located block later (starter thread used)
3. Generally work bottom up. so I rig all the lower mast assemblies before moving up a layer. 
4. On the bow spirit, I generally rig the entire assembly of wood sections together before installing it and make sure all blocks are in place for running rigging.
5. I have not actually used any sort of pre-rigging jig assemble holding thing yet so when I do my stays for example, I rig a left and then a right side while on the ship.  I use a few sections of bent wire fitted to both dead eyes so my cord length is consistent. I do serve the cords prior to installing at the top of each mast assembly using a 3rd hand tool to hold the loop in one end while I whip/serve the middle where needed.
Yes, so my ratlines are done on the ship.  I just took an index card and drew a few lines spaced at the distance between "rungs" and clipped it below my work. I tied a few at a time and took a break.  I tired to keep a little slack in them but was not always consistent.  A jig will probably make it more consistent but I hate seeing all that thread wasted when tying off to a square frame.
6. I pre-rig all blocks to spars and if a block may be in a tough spot, I run a starter thread through it too.
7. All of my standing rigging is tied off at a pin or wherever it should then cut short.  Later I coil a bunch of cord around a pair of finishing nails as a holder and leave a long enough tail to neatly wrap around the pin like it should appear.
Hope that helps. I have an old build log on here where I posted lots of photos as I rigged the Prince de Neufchatel.