Hmmm - that's a good question.
I listened to it a few times and there seems to be several different things happening.
There's a lot of sampled guitar parts on the whole CD - I'm sure Jeff (or Jennifer?) played them all, but for the effect they sampled them and then tweaked the tones.
The very first melody part sounds like a Floyd Rose (or similar) equipped guitar and is probably run through a major overdrive unit (such as a Boogie or Marshall rackmount) plus assorted sound processing units (Sonic Maximizers, etc.).
There is the 'rhythm' guitar part - which also sounds like a sample - and although there's no doubt Jeff is accomplished enough to play it this perfectly every time, it's just the overall vibe sounds like a sample to me.
There is also a recurring power chord (on the 'and' of one and two) that's a sample.
I guess for me the way they juxtapose the vocalizing against the lead guitar lines is the coolest thing - it sure sounds great - and at 2:14 when the bass and the vocals work off of each other. Yumm!
I guess the way you get a sound like this is to be a world-class guitar player for thirty + years and then go in the studio and wail.
foo