What a nice tune, I really enjoyed it a lot Is there going to be some vocals on top of it or is it going to stay instrumental ?
About the low end: I think I heard a low synth pad there and I suspect that it, guitars and bass are occupying too much of the same frequencies. I think the pad might be the biggest cause of muddiness. It might help to play the pad on a higher octave or try a brighter sound for the pad. Cutting some of the guitar bass frequencies away probably would help also. The most muddiness seems to happen in the center of the sound field so spreading things out a little more might also help.
That said the composition and the big picture works very well. Great work, thanks for sharing