Check you screw length so you know how far to drill. Minus the head it's about 42mm, which in practice will be less due to the neck plate. So 42-43mm will be safe. Match your drill bit to the thickness of the screw, test on some scrap wood if necessary.
Where possible, I drill the neck screw holes up from under the body while I have it clamped up with the centre line strung (like above), rather than just mark the holes then remove the neck and use a drill press. The latter increases the chance that a screw could pinch in the body and snap… not a happy place to be.
Holes drilled.
Just to be safe I use a nice strong stainless steel neck screw to cut the threads (ensuring it matches the thread of the actual neck screws). Candle wax and slowly does it… make sure you check how far the screws have to go in and mark it before you start.
Threads cut and actual screws in safely. The reason I do this without the body is that if you have a faulty screw that snaps then it's a lot easier to extract and fix when you're just dealing with the neck heel and not the body as well. Been there, done that.
cont.