It all depends on the body shape and if it has a pickguard or anything, but here is what I did for my Hybrid Strat build:
[list type=decimal]
[*]Mount the tuners.
[*]Mount the pickups, bridge pickup screwed into bridge and neck P90 drilled and screwed into the cavity.
[*]Screw in the bridge, line up the pickguard and control plate and mount the neck, mark the holes for the pickguard and control plate.
[*]Drill the holes for the pickguard and control plate.
[*]Wire up all the electronics, drill the input jack hole.
[*]Drill the holes and install the strap locks.
[*]Fine-tune action and intonation at the bridge.
[*]Done
[/list]
Then of course you can do more set up stuff after that.