im customizing my RG7321 and im getting rid of the neck pup. what would be the best material to use to fill in the hole since it a direct mounted pup? ive heard of several people using cork?
are you refinishing the guitar as well?
if you are, get some hardwood and cut it to roughly the same shape as the hole, then glue it in, and fill the gaps with wood filler, then sand it so its level.
then you can paint over it
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you could just leave it open and paint it a different color like red, that would look awesome imo

otherwise do as Kelaninator said
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Before you cut the wood for the slot, route the slot into a rectangle to make it easier to cut the filler block to shape.

I always use one brand of primer. I think it's Rustoleum iirc.
Block of wood and some wood filler.

Heres one I did a while ago to fill the middle pickup.

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