I used to play Mesa's and been through pretty much all of them. The only help I can give is keep the mids low and play withe treble/Presense I found it very helpful to not have my volume on my guitar on ten and use the neck or middle position pickups. A Tung Sol 12AX7 helped warm it up also as well as well broken in speakers. I went through exactly what your hearing with Mesa's! A 5751 12Ax7 was helpful also. Good Luck!
I should add that I had a DC5 long ago, and sold if and bought a '68 Twin. Best move I could have made. And that's after I had the Mesa modded (for a better overdrive tone). It was just too dark to have decent clean tones.