i won't be much help with petrucci as i don't listen to him but take some considerations into what gear he used and what styles also.
this is very important. *your tone has to compliment your playing style. to try to have a tone like petrucci and cazares, you have to play like they do, otherwise you most likely won't be happy with it.
this includes your band or yourself if you are just writing/recording songs. fear factory's sound and songs rely on a very tight rhythm section of drums and bass as well as dino.
his style as you know involves very low tunings(so tune down to B or A or like dino does on one or two songs drop G), fast double picking, and palm muting among other things. his tone also relies on high output humbuckers(he uses active emg-707's which is like a emg-81), high gain rectifier amps(line6 as his main and mesa boogie as backups), and
marshall cabs for crunch.
alright. with the previous posts suggestions on tunings, strings and what not, try going out and borrowing a POD or
mesa boogie rectifier from a friend or see if a local store will loan one to you. then hook it up to your cab(if you get a head) or your 8008(if you use the pod) and try to find a usable tone in it . use your equipment and try to use a EQ pedal or rackmount if you can to fine tune the sound. if it's not good enough, try the closest amp to the "modeled amp" on the POD if you tried it. you will then have to make decisions on if you want to replace your guitar or pickups to further get a little closer to "that sound".
if you plan on going the line6 amps route. wait until after the upcoming NAMM to buy because there are rumors that line6 is ugrading some, if not all, of their amps. they are said to be using a new type of dsp chip or something and are releasing a new amp soon.
