Ok so made some more progress toward a final setup with this thing -- and I've run into another problem [wiring gurus: see the question at the end.]
First off, I had to do some more work with the neck. The original guitar that ADH and Stereordinary made -- an esquire -- only had a pickguard below the neck, so this thing was overall too shallow for the pocket on the strat with the pickguard. My original solution was thin shims just to get it set up, but stacking a bunch of them wasn't making a consistent angle (they were maple veneer and were disintegrating as I was trying to shape and drill them) *and* the screw holes weren't in the best shape on the neck.
Long story short, after a couple times on and off, the neck screws gave out completely. Time to plug and redrill. And come up with a better way of dealing with the neck in the pocket of the strat body.
So I ordered a 1/8 in thick slab of maple and a several sizes of birch dowel (ended up using 3/16) from Woodcraft (grand total like 15 bucks), then busted out the ancient drill press and followed Dan Erlewine's instructions for plugging the neck holes, which worked great. That done, I traced the heel of the neck on the maple, busted out some chisels, a utility knife, a hand miter saw, and some sandpaper to shape a thick shim that followed the neck heel exactly. This done, drilled some holes a bit bigger than the body holes so the screws would pass through, and plopped it onto a piece of 60 grit sandpaper to hold it in place and took my sanding block with 120 on it and started thinning it down. A bit of trial and error later, I got to a thickness about that of the pickguard and figured let's give this a try.
And voila!
Obviously I need to finish off the end, and I will the next time I have the neck off, but for the moment it's great. Not only does it work (and the guitar sustains beautifully), but the angle I happened onto means I can get the bridge saddles nicely in the lower - middle of their adjustment range. I might fine tune the angle a tiny bit when I shape the bit that's extending out now, but I might just leave well enough alone too.
Generally I'm really happy with how it plays. I was seriously considering abandoning this neck, but this new solution is working really well and the thing is a blast to play. The d-shape of the neck carve, which I was unsure about when the neck was off a guitar, turns out to be really comfortable.
And I'm more and more convinced that I'm leaving the white pickguard on there. It doesn't hurt that this thing now sort of matches my Jag.
In any case, the only thing wrong -- and here's my question! -- is the tone control wiring is still messed up somehow. The six way switch I'm using didn't have any really good diagrams, and I had to add the phase switch for the neck pickup, so I was flying by the seat of my pants. It makes sound in all switch positions, and the volume works correctly, but the middle tone pot does either nothing or very little to the middle pickup, and the bottom tone pot works normally, except it controls the bridge pickup not the neck.
I've reflowed all the solder joints I can reach, but now I'm sort of stumped as to where I might have gone wrong. I can make a wiring diagram if that would help anyone figure out whether the problem is my wiring, or my circuit design.