Sorry to complicate things, otma. I kind of misunderstood your original scheme. Whatever configuration works for you is good. Let's just avoid the harsh zones.

It does makes sense to place the master V up away of your right hand. I really never use it, myself.

It wouldn't be hard to come up with a C (Cap) value for each pos that would make dual caps on P/P's obsolete. You could add P/P pots later if needed. I've used a C value on a few guitars that produces a slight ~1.6kHz peak with the T@4 sweeping up to a stronger ~2kHz peak @0. With that, you can trim the peak as usual from 10-5 (creamy tone at ~7.5), dial in a sweet fat lead tone between 4-5, jangly tones below that to a snarly rock tone at 0. It's a really versatile option. To fine tune the affect, you might need to first try one cap, and then wire another over it.

I have normally applied the above T option for the bridge PUP, but it should work well for the combined pos. You could use it on the bridge PUP if you don't want to bother with the Q-tone. Can always change it later. It might be best to just use a standard C value for the neck for jazzy bop tones when you want them, but whatever works for you. That L609 is a sweet mellow PUP. I can give you my suggested C values if you want. I posted some samples of the option on a bridge 4.8H L610L. Look here for samples labeled "TSG D&S(JM~) L610L T@10-0...": https://app.box.com/s/dkm6g4my1z2nsx7tz0d1

You probably want to use a pretty low C cable ~200pF so you can get some extend highs with the T's opened up. They will also have a more substantial affect from 10-5.

The 4-way rotary sounds like a good choice if you can wire it that way. You know how it's configured? Just send wires from each pos off to each T.