I was listening on the drive to work again today, and really, he's got some GREAT tone on that album.
The rhythm sound I'm actually pretty close to - it's basically your typical prog-metal Recto sound. Lead, though, I can't quite get. It's a little more middy and "warm" than is really the norm for a Recto, but the things are so fucking tweakable I don't know if that's because he's setting it a particular way, or because he's using somehting else.
My impression was that the whole thing was cut with a Road King, so is what I'm hearing the difference between the stock solid state rectification and "bold" setting on the Rectoverb vs. a Road King in Modern, set to tube rectification and "spongy?" Or is it an altogether different amp?
Petrucci sounds like himself no matter what Mesa he's plugged into, so it's tough to say, but I guess it also shouldn't matter, should it, if he can do it...?
I think it's a Mark II/IV.