Well, I have a JCM2000 DSL head and I like my tone very much

... here are the settings:
Deep - Off (Brutal for hard riffing)
Tone Shift - Off (sucks anyway)
Presence - 5.5/6
Treble - 5.5/6
Middle - 7
Bass - 9
Reverb - 10 (I really like reverb

)
Volume - Low... can't really crank it. If you turn it up, you should lower the treble and presence controls...
Gain - 9
I also use this settings for rhythm and frankly think Mesa's are too dry sounding. They ARE better for DT type thing, but for solos I prefer the Marshall, also they sound better in rock for me...
For example, I prefer Satriani's tone against Petrucci. Although I like them both, for me Satriani has a warmer and sweeter tone... if you like Petrucci better, then find another amp, the Marshall will never give you that.