So does every single future screw site need to be pre-drilled? How big of a drill bit do I use? How far down? The length of the screw, a bit shorter? I have no idea
Drilling is generally done before finishing. For most holes, measure the shaft diameter of the screw not including the thread, and thats your drill bit size and drill the full depth of the screw.
is it OK if you drill after finishing with Lacquer paint? If so, would you use masking tape on the area to be drilled? That what I used to do when hacking up computer cases.
Sure it's fine. It's just easier before because you don't have to worry about marring the finish. And before you finish ALWAYS do a mock up, meaning, entire guitar put together, strung up, etc. That way you don't go "oops, didn't route that cavity deep enough. Too bad I already painted it"