Preamp tubes can possibly help.
V1 with the Svetlana 12AX7 tube, I found this one works very well with the clean, and aids on some tone correction for the other two channels. It has just a bit of less gain than the Mesa 12AX7 and a different vocal sound. For V2, Tung Sol 12AX7 is an improvement but I may have been after more gain, more so for correcting the bright shrill of the edge mode.
If you want to drop some gain on CH3 with a mild approach, The JAN 5751 tube does a decent job in V4. That has the last high gain stage in the lead drive circuit. I did not state if it was a Phillips, GE or other as the JAN 5751 can be expensive. I have not tried current production version to relate. The JAN/Phillips 12AT7 in V4 will work too but will darken the sound a bit more.
I have used just about every tube in current production in the Mark V90, only because I could not find any channel or mode that I cared for.
V3 is the last stage following the lead drive, and tone stack of the other two channels. A good quality tube here matters. Mullard long plate 12AX7 or CV4004 (medium plate) can aid here. I have also tried the Svetlana 12AX7 tube as well (very similar in appearance to the Mullard CV4004 or Tung Sol 12AX7) but has a different tone and gain characteristic. Another option is the JJ ECC803 which is a long plate version of the ECC83s (Mesa standard 12AX7 tube).
V6, does not matter much. Part of V6 is used for voicing CH3 as the last gain stage in the signal path before the GEQ. Stock or other will do fine.
As for the Phase inverter, that is more to taste. Stock tube is fine, Mullard long plate adds more balanced tone, Sovetech LPS is similar but a little less in the low end.
You can get some interesting response with different preamp tubes in the Mark V90. I tried doing similar things with other amps but it did not seem to matter as much as the end result was not much noticeable. What I liked best in the Mark V90 tubes have been long out of production since 1994-1996, the Mesa branded Chinese 6N4-J Beijing Square foil getter tube that was commonplace with the Mark III amp. It is one of those 12AX7/7025/ECC83 replacement tubes. They do a really good job in the V3, V4, V5 and V6 positions. It tightens up the tone a bit so you avoid some low end swamp if you like to dial in more bass. Overall, they improved clarity and note definition I was not getting with the stock Mesa tubes (JJ ECC83s) as that was too much ice pick for me. My Mark V90 is a special case amp, Only available to the lucky few, it is the limited edition Lemon Ice model. It is just the general run of the mill production from 2012 that fell sort of excellence and has been terrible to deal with so tube rolling became a standard practice with that amp to see if anything could be done to compensate for the excessive brightness and other noisy issues.
