This is gonna take some time to get right. I haven't been through it all yet, but I'm having a problem in that, on the pole of the 5-way where the pickups are connected, I can't see what the common lug is wired to.
In any event, your description says "Neck Phase", but it looks like the bridge pickup gets the phase switch. The phase switch won't work as shown. You have the black wire (+) from the pickup going to the 5-way switch first, and then to the phase switch. This will simply ground out the pickup. The phase switch, whatever pickup you put it on, will be the first thing in line out from the pickup "Hot" wire goes into the switch, "Not Hot" wire goes into the switch, two leads come out of the switch. from there, one of the 2 leads goes to the 5-way switch (or, as shown here, to a blend pot)
Anyway, let me dig a bit deeper tomorrow, more later . . .
It'd likely help if you could write out a bit more of what you are going for with each control. Also, is it intended to be SD or DiMarzio colours? Are the dashed grey pickup wires the bare shields?
Is the dual gang pot on the phase switch doing the blending? Weve seen dual ganged push/pulls. Also, have seen dual ganged blend pots on guitars which are best with a special taper that is reversed in direction between the two wafers, and zero from one end to mid turn. That way you can get a full volume sound from both mixed. But can you get all that with the switch too?
That being said, Ive never tried them - have you tried this part of the circuit on other builds?
HHH with its six coils, can get as complicated as you want and there'd be about a million combinations possible. Obviously Yogi knows exactly how many, but may prefer to keep that info to himself.
But, im interested in your opinion, since you work on a lot of guitars, talk to clients and also play. What would your overall philosophy be for designing a versatile but practical wiring for HHH, where the right useful tones are in the right places? There's a balance between versatility and simplicity, and my views change over time, but are based on more pondering than on real world experience.