MetalGarret
Inspired
Usually when things like this appear there's only one thing that can be the reason. And I'm sad to say I mean it's the player himself. Ears and playing style are things that no amp tweaking can cure.
I hated JPs new album tone in the full band mix and don't like it here either. I don't suggest you match his tone here since it's definitely not his best.
For what it's worth I love Petrucci's other tones a lot. For that tone I suggest you use OwnHammer Free Beta Bogner IR's or GuitarHack's impulses. Those sound just like JP. Maybe a bit more bite in the OwnHammer.
Well the goal was to take the best that that tone had to offer then brighten it up a bit and put my own touch on it. I'll look into Ownhammer when I get home.
I should also mention I'm using this for recording an album. Not playing live at the moment.
I know how to play my guitar. That's out of the question.