Ok I tried out some of your suggestions, and a few other things.
-Re-ran the drums through the hardware saturator again so it doesn't distort on the busy parts.
-Tracked through the Badlander 100 instead of the Engl and boosted with a Silver Archer pedal.
-Put a dynamic EQ on the pokey part of the bass (around 2.5k) to keep it at bay.
-Got rid of the SM57 and re-mic'd the cab with an sE7 condenser and MD421.
-Backed off on the limiter so it's barely limiting every once in awhile.
I think I'm liking the Badlander better for this track. Of course it's a 100 watt vs the Fireball's 25, but it's just got some extra weight and authority behind the riffs. Overall I feel like these changes have cleared up the clutter some on the track, but I'm still gonna try to dial in the guitar sound some more.
A friend of mine that's the recording and mixing engineer for Crowbar, Exhorder, and Down's latest albums is going to work with me and help me get everything dialed in better this weekend, so hopefully that'll help too. He gave me the idea for swapping out the 57 with the sE7. He also suggested blending in a DI which I don't have but will try next. Let me know what you guys think and if you have any more suggestions, thanks brose!