Im using a tele humbucker pickguard and bridge.

The string thru holes will be drilled before finish. But should I drill pickguard, control plate screws, before or after the finish?

If I were to drill these holes prior to finish, should i fill them with wax to prevent water from getting in and raising the wood?

Thanks a bunch
I would just drill them post finish. I did that one a finished strat once. Have never had any problems. If you drill before finish, its likely that your finish will cover them up any way. just use a small drill bit as big as your screw (minus the threads) and screw the screws down. all it takes. only holes that you'll want to drill pre-finish, imo, are the string through holes and the neck bolt holes.
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I advise drilling everything before you paint.
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Granted I'm on my second guitar, but I would do them before hand. What if you slip or something while drilling/pulling out the drill bit, scratch the surface by accident, etc. I drilled all the holes first, pre-sanding. Just my opinion on the matter, accidents do happen, and i'd rather it happen on an unfinished piece of wood than a finished piece.
After doing my first build I'd drill them post-finish. Why? As I was wetsanding the finish water seeped in the screw holes, raising the grain and the finish and created some burn through around the holes. Granted, most of it will be covered up by the pickguard, but it dosn't look very pretty.
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I'd do it post and use masking tape to prevent the finish from cracking and/or getting scratched.
Definitely after if you can. But stopping the water from soaking in is all you really want to do, so you can do it either way.

The wax sounds like a good idea, but personally, I'd wick some super glue into the bare wood before applying wax, just as a little extra insurance.

And I've heard that using mineral spirits and mineral oil instead of soap and water to wetsand won't raise the grain. I've never tested that, but it makes sense.