Are you low/high passing the guitars any? I found that helped a ton on my mixes. If the guitar and bass are playing similar or the same part, let the bass do the "work" and provide the lows. On my eqs, I usually cut all of the lows out of my guitars from around 230 and under. I can't remember what I cut out of my highs. But that just may work for my situation. Also, are you double tracking? Quad tracking? If you're layering multiple guitars, all of their eqs and gain will build and cause mud. What you want to do in that situation is lower your gain on all of your guitar tracks. With all of this hi/low passing and reducing the gain, your guitars will sound tiny and icky on their own(God knows mine do), but when you add them all together and then have the bass driving underneath, it'll create a solid, clear, and cohesive sound. The tone on that particular song sounds slightly scooped in the mids, so you may want to try that as well, BUT BE CAREFUL. The golden rule I've come to live by with guitar recording is that moderation is not only key, it's the freaking door, too. That goes with eq,gain, compression, reverb, everything.
Also, what kind of gear are you using? A pod? AxeFX? Amp Sims? I've got experience with a lot of them except for the Axe.
Here's a clip of some of my stuff so that you can judge my advice as helpful or crap.
http://dl.dropbox.com/u/38852223/Progressions.mp3