Are you using brad point bits, fostner bits? I would mark and drill the holes on the body(use the plate as a template). Then put the neck on and using a brad point bit that fits snuggly in the hole on the body mark the neck. It will be a perfectly centered mark for the slightly smaller bit you'll use to make those smaller screw holes. Also something you don't read much about is that a depth stop in the drill bit helps a ton. Good luck!