Hi Andy, as Brendan said photos of the problem area would be handy so that we can better understand what you are dealing with.
If on the bottom/floor of neck pocket delicate chisel work and light sanding should work, just need to make sure everything remains flat and in the same horizontal plane as the top otherwise neck break angle could be compromised.
If on the side i would also delicately chisel down vertically and then lightly sand being careful not to take off too much timber as you still need to keep a fairly tight and uniformly shaped pocket for securing the neck once bolted on.
500k ohm pots are the go and i always use audio taper for everything including tone as the roll off is more gradual compared to linear. Kit would have come with 2 x vol marked 'A' and one tone marked 'B' where the B is a linear pot. Another upside of using same type of pots is that it doesn't matter if you wire up the wrong one as they are all the same and also interchangeable if one becomes faulty. Suggest using mini pots as the control cavity is small and very tight fit with all those wires. Have mostly used bourns which have good push/pull pots for coil splitting and have also used CTS on a Tele and Alphas on recently finished ES1. Hard to tell any difference soundwise for same value ohm rated pots. CTS tend to be the more expensive ones.
If you use the tone control upgrading kit capacitor is recommended. No need for treble bleed mod if keeping the J Bass wiring as it doesn't seem to work without a switch between pickups.
Hope some of this helps.
Cheers, Waz

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