Ive notice on Schecters (not sure if its all guitars) that if the action is too low, pinch harmonics are hard to produce. So maybe try raising the action a little bit.
I have them in my Schecter Damien and I like them a lot more then the actives. I think they are a bit more versatile. Might be a tad bit muddy in the neck, but you can easily fix that. (amp/pedal eq wise)
Id go with something more along the lines of HSS with a coil tap, best of both worlds if you ask me.
I really like those hardwire pedals. Ive never used one to push tubes before so I'm not really sure if they are what you are looking for, maybe just a gold ol' Tube Screamer?
The Devil Wears Prada
Guthrie Govan
Jeff Loomis
John Petrucci
King Crimson
The Mars Volta
Get a Boss Metal Zone

or those new digitech hardwire pedals, I was really impressed with those.
The other guitarist should play an F Major sweep, If you wanted to harmonize with a B minor sweep, youd play a D Major sweep
Dusty Waring of Between the Buried and Me. Not really a full fledged rhythm guitarist, but the dude is insane.
Its just how many notes are in between those two notes, while staying in key.
sounds like a lot minor and minor pentatonics, and Diminished stuff. Not so much diminished scales but more Diminished arpeggiated sequences
I think, from a musicians point of view, BTBAM is a great band. The way they mix elements of Jazz, Ambiance, Latin, and good old Prog Metal is just amazing. Some of the guitar work is just ridiculous and still blows my mind. It leaves me thinking, "how would you think of doing that, let alone physically do it." No one can dismiss all of the members skills on their instruments.
for gigs i use a friends ampeg half stack. on the pedal my settings go..
Level 1 o'clock
treble 1 o'clock
bass 1 o'clock
mid 11 o'clock
mid freq almost 12
and distortion at about 1 to 2

i really dont like this pedal, im pretty much set on a new pedal. Just dont know what one

EDIT: its not the amp, the amps clean tone is awesome.
Ive been looking at the boss mega distortion. But I think it might be a little over the top gain wise. Im not really into metal anymore so i dont really need a metal pedal. I just want a new pedal that I know can handle metal if I ever want to play metal. But I mostly want it for a good heavier rock type of tone.
Ive had the Boss MT-2 Metal Zone pedal for almost a year. I still love the sound this thing puts out but on stage it just doesnt cut through the mix. I need suggestions on a new distortion pedal. Im heavily influenced by Thrice so I guess im going for that kind of sound, very dynamic but heavy and light when i need it to be.