I'm building a guitar from scratch, and right now I'm trying to drill the holes for bolting on the neck to the body. I have the neck pocket cut and the neck fits in snug, but I can't find a good way to mark the holes for where the screws will go. I tried putting nails in the screw holes on the neck and making small marks with them, but they had to much play and ended up being way off, costing me alot of filling. Anyone know any methods or tricks for doing this?
Just measure it out man. Measure the neck heel, draw it to size, do the same with the pocket. From there, you should be able to measure out where the holes go in the pocket.
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With the neck in place, you can just drill through both the body and the neck at the same time. Use a piece of tape on the drill bit to mark the stopping depth.
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screw the screws you are going to use into the holes until the poke out the other side by around 2/3mm, put the neck in and press down hard

then use a pencil to lightly shade the area that the marks are, this will make the show up lighter than the wood around them

i just finised a carpentry course, i did these sort of tricks all the time lol
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The reason I was having trouble was because the neck has predrilled holes in it already, but thanks guys I got it figured out.
I like to have the tailpiece installed before I set the neck's position. Aligning the neck's easier for me if I actually put the D & G strings on and use them to align the strings to the fretboard's inlays to get the neck straight with the tailpiece from the nut on down.
Drilling slightly oversized holes in the body will allow a bit of play in the neck's location when you screw it down to help make the alignment easier if your using a 4 bolt neck plate. Good luck.