Sounds like you have a good grasp of this type of thing. Could you elaborate a little more please? Even with my guitar, on Mesa amps (JP2C, Recto's, IIC+) I still have a little trouble with getting that really tight, percussive, low-note palm-mutes like Petrucci gets. I can get it no problem using my (real) Tri Axis or Dual Rec, but in the Axe, I actually tend to use different amps. (I'm pretty sure it's just my headphones, but until I get the monitoring setup ironed out, they do the trick. And do sound great, overall.)
The best way I can describe it, is even when I choke up past the bridge to the point that the note sounds about 1/4 step sharp, there's still this 'flub' that lingers, kinda like a rubber band. The 'chunk' comes through, but that flub stays with it also, as opposed to getting choked off. It's subtle, but I'd love to dial it completely out.
I've tried dialing the MV way down like some have suggested, rolling off the lows, drastically cutting the bass, and even all the deep-dive parameters I don't really understand. It's really close however, just not 100%. I also use a global EQ as a headphone correction curve, but I haven't yet tried using EQ like you said above, pre-amp block. Can you recommend specific frequencies, Q's and dB's to try?