First off, thanks for the compliments!
But dude, I'm having the same exact problem with the Timeworks compressor on my toms and various other elements in the mix. I don't even have it limiting, I just stuck it on the 2buss to keep my overall master at 0.0 and it's still doing funky shite to my sounds, dunno. We gotta sort that...
As for rhythm guitars, it took a LOT of creative EQ'ing to get 'em sounding decent. I also set up an aux send with RComp and send a bit of the Guitar Buss to it for a little extra kick and consistency.
As for bass, the basic sound was great, so the only EQ I did was a HPF at like 30hz. I did however run the bass track through Amplitube to dirty it up. Adding that grit really helps the bass stick to the GTRS. Too much and you'll have a sloppy mess so, it's just about experimenting.
BTW, I dig your mix. Did you use GuitarSuite as well?
Charlie