Finished! (For now)
Daniel came back and said "yeah, it sounds really off at the 12th fret". With visions of "oh, crap, we have to mill off that fret and move it" we started playing with things, and discovered that the bridge was in the wrong place. The bridge had individually adjustable string positions, so we moved them, and got a sound that was okay, but the bridge was also really too high.
So I chucked it up in the milling machine, milled it down a bit, then tried to clamp it at an angle to put a bevel back in some of the pieces, and of course that caused the whole thing to flip out of the clamps and be munged by the bit and... yeah, it was ugly.
With no place to buy a replacement bridge open yet, we decided to make our own, out of purpleheart and some strip brass I had around, and lo and behold it let us put it in exactly the right place, and sounded awesome! What's better, there's enough room in the frets and vibrato in Daniel's playing style that the micro-adjustment didn't matter, he was playing with the sound all the time anyway.