I just had the same problem. I was getting microphonic squeal on Channel 3 (except mine squealed no matter what volume) in Mark IV mode and a little bit on II C+ mode. So yesterday I made a trip down to the music store, bought a couple of 12AX7 Boogie brand tubes, and about thirty minutes ago switched out the preamp tube position V3... and that fixed it.
Below is a link to an older forum post I referred to. That member switched out V1 to fix his, but I guessed at V3 after referring to the diagram in the manual on page 62 and looking at which positions were what gain stages. I got lucky and guessed correctly.
http://forum.grailtone.com/viewtopic.php?f=33&t=37571
Hope this helps!