I think speakers and the GEQ shape play key roles in getting his tone (as well as his fingers). I have a harder time getting a SFAM type tone out of my EVM speakers, but the Emenince V30 clones in my Orange cab nail it since it's very similar to the Mesa recto cab Petrucci uses.
The middle slider on the GEQ has to be just right as well, what I did was just play a song off Scenes From A Memory on the CD player while playing along and finding the sweet spot. It's just about 1/4 above the bottom line give or take; it's very sensitive. Then a V shape for the rest, I put the first and last sliders at the top line, and the other two in between the middle and top. Petrucci uses a bit less treble though.
The settings I use from left to right are
7 pulled
7 pulled
0
5
2
7
6 pulled
presence 2