Hey Groovyman.
re: runs - I thought I posted this in your thread, but it was a another members recent thread. Anyway, check out post #31 HERE.
I describe a couple of methods for dealing with drips/runs etc you may find useful.
With poly, I give it a minimum of 10 days, 14+ if you can stand it.I should get to 50 coats before the weekend - how long should I leave it before finish sanding and buffing? Is there any reason to wet sand? Or can I go dry? I'm concerned about swelling...
The old school way of checking the level of cure, is by putting your nose right up to the timber and giving a sniff. If you can smell any solvent, it not's fully gassed off. However IME, 10-14 days has been fine with poly, and 3-4 weeks (or more!) with lacquer. With either, longer is always better.
Wet sanding will be required if your going for a high gloss finish. Dry sanding is only going make it look quasi-satin.
The way to think about the difference is, wet sanding has a greater polishing effect and dry is creating micro-scratches.
The whole wet sand before drilling holes or after is a subject for debate that has been knocked around here a lot. There are reasonable arguments on both sides, so it comes down to personal preference. Some times you don't get a choice if the body has pre-drilled holes, it just has to be dealt with. Since your build has some but not all holes drilled you can get the whole experience and compare!
I tend to be in the drill before camp, but that aside, what I would suggest in your case, is leave your pickguard holes etc undrilled until after you've levelled and polished. Hand-applied poly is generally more forgiving to a drill bit than lacquers IMO.
Now for the existing holes and cavities:
(after last coat and before wet sanding)
1) Plug any existing holes with a small amount of bee's wax (you don't need to jam pack the entire depth, just enough to "cap" the hole).
2) Apply a few coats of shellac (or wipe-on poly) to the inside of the cavities. Just enough to seal & waterproof the walls & floor. This also provides a better surface for shielding tape to adhere to IMO (if you're planning to do that).
An added benefit to the bee's wax is it works as a lubricant for the screws when you turn them in. Any excess wax that may smear on the finish while filling the holes or after turning in a screw can be safely wiped off with a small amount of naptha on a rag.
Hope this helps...