Just as a follow up. This guitar seems to be fairly stable now. I took it down yesterday to have a quick noodle and it was reasonably in tune. The intonation on the 6th isn't quite right (based on fretted @ 12fret. Harmonic is better) and there isn't really anything left to get out of it, so I probably screwed my measurements up slightly. It's not far enough out for my ear to hear it, but still a little annoying knowing I didn't get it quite right.