Is the cap leg on the 2nd tone pot going to the outside lug instead of the middle? It looks like it may be, but it's hard to tell from the photos.
Also, is it possible the tip of the red wire poking through the switch lug is brushing the switch body tab? Again, difficult to tell from the photos. And, the hot lug on the jack looks close to brushing the copper shielding in the 2nd pic, but again it hard to tell. Plus, all the ground connections on the back of the volume pot are a touch gnarly, so there could be a bit of noise in there.
All controls working independently without noise... The only minor things are still when zeroing either of the volume pots when both pups selected kills all volume, and with both pups selected with both volumes fully open there is a slight volume dip compared to solo’d pups... however, I’ve noticed that if i knock the neck volume down a notch then the volume boosts back up to same volume as when either pup is maxed out. Not issues, just oddities.
The build is now officially finished (whoop!) and I’ll try to get pics up on the build diary later today.
No noise when one volume pot zeroed with both pickups is standard with that wiring arrangement. It's what I'd call 'Gibson' wiring and all twin pickup Les Pauls, SGs, Flying Vs etc. have the same issue. One reason there's a pickup selector switch! for when you only want one pickup on! I think the Rickenbacker wiring method prevents this, but it is more complicated circuit and needs a different type of selector switch.
The 'both pickups on' volume issue is down to phase cancellation, and lowering the output of one pickup reduces the cancellation, actually making the output louder in this instance! If the pickups were fitted in slightly different locations on the body, you'd get another set of output interactions which may result in a thinner and quieter, or louder and thicker, mixed sound. And changing the pickups for ones with different tones is also going to give a different mixed position sound.
If it really bothers you, then I'd suggest playing through a compressor, set with just enough compression to help balance the levels.