I revisited the wiring briefly last night and it all looks OK, so I suspect you've hit the nail on the head.
The guitar has a fair bit of work left before I'm happy with it, but I'm not going to do anything with this until I get around to doing the pup swap. When I do that, I'll bring over the LP's stock pots.
Progress shots:
The hole refill is better but not perfect. I need to fix the action - I noticed some funkiness around the 15th fret on the 2nd string. If I bend up, it's dead. I can fret the 3rd on the same fret and it's fine. Obviously, I also need to trim the strings :P