Personally, I drill all holes after finishing. But I'm usually pretty confident I'm not going to drill in the wrong spot (I double, triple and quadruple check EVERY measurement). Drilling all your holes first means you can do a complete dry build and string it up to make sure everything is where it needs to be and fixed before finishing if needs be. For your first, I think it's probably a good idea. If you need to move the bridge or something, it's going to be a lot easier to hide the fix.

To enlarge pot holes, I use an appropriate sized drill bit in REVERSE and with no pressure other than the weight of the drill. If you can get a piece of wood underneath the hole to drill into it will lessen the chance of tearout. Or, safer alternative, get yourself a reamer, like this one