Sort of accidentally started a new build...

[Simon Barden]

Is the idea to get the holes sitting in the middle of the slots, or won’t the nut screw down far enough into the tuner body because it’s run out of thread? If the latter, can’t you cut the screwed end of the nut down a bit so it will screw in?

[McCreed]

Is the idea to get the holes sitting in the middle of the slots, or won’t the nut screw down far enough into the tuner body because it’s run out of thread? If the latter, can’t you cut the screwed end of the nut down a bit so it will screw in?

That's a good question and proposition Simon.
I have had to do that with a few non-Fender necks due to the headstock being slightly thinner. I found using a dremel with a cut-off wheel the easiest and cleanest method.