I listen to hard rock, metal etc. Everyone says you should play guitar with less distortion than sounds right w/ guitar alone and it has always held true for me, even when I've been very skeptical. Try dialing down the gain some and see if it helps clear out some of the mush.
I can't give expert advice on how to mix clearly, but I can say as it stands it sounds like when you go to a hard rock/metal live show and the room just isn't built to handle the sounds so it all sounds unclear. I think the reverb on some parts (or natural room ambience?) is set too big b/c it sounds like the recording took place in a warehouse.
The clean guitar at the break and end is too quiet. Actually compared to the awesome hard parts, the clean guitar part in the break is pretty standard. It sounds like your just messing around on a couple major chords which does nothing for me personally. Those soft breaks are really a good place to do something special. Right now, it literally sounds like your just taking a break.
Lastly, volume levels seem to go in and out, not systematically, but dependent on what your playing. Maybe try compressing the individual tracks and/or master bus.
It's also worth messing with your EQ independently on the softer and harder vox. Try lots of different settings to see if something helps enhance the overall sound or get out of the way of the other instruments.
This could be a really cool song once the aesthetics are optimized.
Kerrio