Mine has a pair of 5881's in it, instead of the usual EL34's for some reason, and they give quite a bright sound, not exactly "modern", but it's not your "normal" Marshall tone. Maybe next time you change the power valves, try putting a different power valve type in there, a lot of Mesa amps use 6L6's don't they?
Also, changing your pre-amp valves for something more "modern" will shape the tone as well. I bought some Sovtek 12AX7 WC's from HotRox, which gave the amp a very "modern" tone (to my ears anyway), which I wasn't after, so I replaced v 3 with an older ECC83M to give it that older sounding vibe. Find out what valves they use in the V-Twin from stock and put some of them in.
Just a thought...