OK, so I gave up on the Mega Strat project. As I said before, I am no expert when it comes to guitar wiring, but I have replaced more than a couple sets of pickups, replaced switches and pots, and did a complete rewire of my Peavey T-60 without any trouble. I haven't ever had complete failure as I did when wiring this project up... The more times I desoldered and resoldered, the uglier things got, the closer new parts come to getting burnt up and failing.
Here's how it panned out:
I have the Custom Shop '69 pickups wired in as standard with the middle pickup flipped (at the moment). I wired in the modded TBX tone control as a master tone, with a dummy knob (not wired to anything) in the third spot. It sounds great, looks great, works great.
I'm a little concerned because I have a very limited usable range on the volume pot. It was recycled from some previous project, so it may be burnt up inside or something. From 0 to 6 it is completely silent, from 6-10 is the normal volume range. I will pick up a new 250K pot next time I am at Ye Olde Radio Shaque.