The way I did it once:
Clamp the neck to the drill press so it will not shift. Align the table on the press so the drill is centered over one hole. Place the body over the neck, make sure its seated as it ought to be, and make sure things have not shifted. Drill that hole. Unclamp the whole affair and try the fit, attaching the neck with a neck plate and single screw. Assuming nothing shifted, the screw will be perfect, holes properly aligned. Mark the rest of the holes from the neckplate.
The other way to do it - just fill all the holes on the neck with maple dowel, drill the body using a neckplate as a template and drill the neck from that.