Hi Andy,
I'm having my dad prepare a new set of electronics for you. Can you test and see if the extreme rotation of the pan pot (at the far ends) causes any change in the sound?
These are your electronics:
You'll get new parts when the green indicates (circuit card, pan pot, bass and treble switches). We are thinking that at a minimum your pan control is defective.
As far as the nut goes, if you need it lower than it will operate, we'll need to either modify what you have or make new parts. Either way, we'd need the whole bass here. You might be able to sand the bottom of the baseplate locally, but sanding through chrome plating takes a while!
I noted that I thought your bass was one of the best setups (among our already awesome setups) that I had seen. It just was really very easy to play!