Well, I dropped the pickups into the guitar tonight and the spacing is perfect. In fact, it's better than it was in the "correctly" spaced guitar! Weird. Anyways, I've had a bit of a play and the intonation need some serious adjustment, plus I need some new pickup screws, because the neck pickup won't go high enough. Sounds pretty good so far, though. I'll post some clips when I have it worked out.
The only thing is that the bridge humbucker is really thin and wimpy sounding. It was cr@ppy with the burstbucker in it and I thought it was just a cr@ppy pickup, but the warpig is also really thin and weak. That's not right! I will start another thread about that, though, and also post a clip when it's working properly.