If this is an option.. most assuredly... do it that way.. the reason... you get to choose where the holes will fall on the back of the body, thus dictating where the neckplate will be positioned... If you allow the position of the holes to be determined by the existing holes in the neck.. you wil not know how the neck plate will be positioned until it's too late. It could wind up as crooked as the fairways at Deepdale in NY...Another vote for plugging the existing holes and starting from scratch.
This, only with @garymaddox's shorted, sharpened screws.I used trim nails with the heads clipped off; wrapped tape around them so they were somewhat snug in the neck and wouldn't slip out; then pressed the neck into position, and drilled where the marks were using a drill press. Worked like a charm:
I also agree with tiskit86, plug the holes first.Plug the holes in the neck. Drill them out a little larger than they are now, and plug them with maple dowels the same size as the bit you use. Sand 'em flat. IMO, this is the easiest and best solution to get everything fit right.