Hi Ken,
Without being there to look at the amp, here is where I will start:
1. Where do you have the Bass set on the Lead channel? I could not turn my Bass on the Lead channel above 4 without getting similar results. This is due to the placement of the EQ in the signal path. It is directly after the 1st gain stage. This is why I switched to the DC series amps, but the Mark IV is a sweetie.
2. Have you changed the Preamp tubes yet? It could be that one of them is making the sound and it falls out of the frequency response of certain Power tubes, or is causing the Power tubes to distort in an unpleasant way.
3. I would replace all Preamp tubes 1 at a time and try the amp. I would use a known good tube from another amp if you have one. Then, after you isolate the problem (assuming this isolates the problem) you will know exactly how to fix it if it happens again.
4. Then, I would call Bob at Eurotubes and order the High-Gain re-tube kit. This did wonders for the tone of my Mark IV. I used it with 6V6's for a while, but didn't like the fact that I would destroy my tubes if I accidently bumped some of the settings on the back. The tone was phenomenal though, not Vai like at all, but extremely Bluesy.
In the end, before I sold my Mark IV, I was using 6L6's in the inner sockets and JJ E34L's in the outer sockets. The E34L's are by far my favorite for their tone and durabillity, more Hi-Fi than standard EL34's.
Hope this helps, if not, PM me and maybe we can look at some other things.
Mesa is very helpful also. They can't believe it when I tell them what kind of following the older amps have. They are very busy, so sometimes it takes a few hours to return a call. Mike B seems to know the most about the Mark IV's.
Andy