Hi Kris, when drilling any holes it is best to line up the length of the screw on the drill bit and then wrap a bit of masking tape around at the point you want to stop drilling. For example, scratch plate screws may need a 2 or 3 mm bit and depth of around 7 - 10 mm.
If the holes drilled are too small or too tight you risk either slipping off a screw driver and marking the guitar, or even worse, breaking a screw off in the body. This actually is more prevalent when doing the locating screws on headstock tuners. A handy tip is to also roll the screws across either bees wax or slightly damp piece of bath soap so that acts as a lubricant for when screws are driven into place. If there is too much effort required when tightening up a screw it may end up snapping off, particularly the really thin ones for securing tuners.
Being a P Bass the only tricky part is locating the bridge. Personally, I would leave that until last when doing final assembly as the bridge plate holes will be slightly bigger in diameter which could trap water and cause swelling when doing any wet sanding. No real point doing strap button screw holes unless you want to screw in a hook at the bottom to help with hanging it up to dry. Again, not my preference as it just complicates finishing around an object that may end up attracting drips and runs. Would seriously consider drilling neck for the bolt-on screws but that is also just as easy done later too.
Cheers, Waz