Hi Brian. Have you had the kit a while? If it's only just arrived, the wood may settle down after travelling. It did a lot on my ES-3 (though it did travel many thousand miles) and took about a week.

Before it sorted itself out, I was wondering how best to try and determine which bit needed sanding to get everything fitting well, but I never really came up with a plan that I found satisfactory. Have you tried clamping the neck (as if glueing it) to see if it improves under pressure? If it can be forced together, then maybe leave it under pressure for a few days to see if it will stay that way. If it can be forced together, it should hold when glued, though it's obviously better if it fits nicely in the first place.

Otherwise maybe try fitting a small set-square around the neck heel to see if that has been cut straight, or measure the depths, front and back, of the body neck pocket to see if one side is slightly higher than the other (plus measure the corresponding neck cutaway depths to see if they match.

I had thought on mine of maybe trying to get hold of some thin carbon/copying paper, slipping that into the joins and seeing if it marked where things touched and didn't mark where they didn't, but I never had to do that in the end.