So I got my squier neck in today for the 100GBP build. The bolts don't line up..

Is it better to fill and redrill the neck, or the body? And what is a good fill/drill material? I used some wood filler on the body for some parts and it doesn't seem that hard enough to accommodate a screw without cracking or something.
if i was in that situation, i would re drill the holes in the neck.
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Using wood glue to stick dowels into the existing holes in the neck. Once it's dry you will essentially have an undrilled neck. Then just drill the holes in the neck heel to match the body and you're good to go.
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You prolly don't need to fill anything (unless the new holes will be really close to the old ones). Drill pilot holes with bits slightly smaller than the screws you'll be using.
It depends on how close the new and old holes are gonna be. I have used wood filler on neck screw holes without problems before.