The undersize of neck bolt holes in the body is very useful for marking the hole positions in the neck. With the neck clamped in position you can either use a drill that fits the hole to mark the neck (be very careful not to cut into the body hole wall) or gently tighten the screws until they just mark the surface of the neck. In either case use a drill press (if available) or great care drill the "tapping" holes in the neck (make sure you don't make those holes too deep), and the clearance holes in the body - these two sets of holes will be different sizes, I think it's 3.5mm in the neck and 4.5 in the body.