Okay, so I recently picked up a 1968 Ovation 12-string hollow body electric guitar, which I put a whole new electronics kit in and cleaned up a couple weeks back. I've been tinkering with it ever since trying to get the setup and intonation right. The low E and A strings had a lot of buzz since the nut slot was worn down pretty good, so I worked in a shim and got the action set properly today.
Problem is, I still can't seem to get the intonation right. I can get the strings all tuned up (according to my Boss TU-2), but the sound when played together is awful, and the strings are not tuned from one to the other, regardless of what the tuner is telling me.
Is there a special trick to setting up an archtop, or a 12-string specifically? My tuner is working fine on all my other guitars - do I need something different to adjust this one?
Here's a couple pics of my baby:
