The whole thing sounds a bit muffled to be honest. Surprised I was the first person to point that out too.
Well, the overheads were the only thing that didn't sound muffled , or at least not too badly but the rest (guitars, snare, bass guitar etc etc) are just lacking in the higher frequencies.
You can definitely get away by adding more "air" to the guitars (adding a bit of "fizz" but the good fizz, not bad fizz) and the snare could definitely benefit from some more attack frequencies.
The fake bass is just crap man. Buy a real bass, borrow one off someone or whatever, because your current way of doing bass is only just contributing to clouding the mix up.
As for the guitar being out of tune, well, fuck, Meshuggah used to use a 52 for Bb and never had that problem and I use 56 for A and don't get that problem man. You need to take care with the picking hand, because 52 should be plenty thick and have enough tension for C#.
Just keep A/Bing your mix back and forth between the original song and you'll hear what I mean.
The guitars in the original song are somewhat 'muffled' compared to the likes of say, the This Godless Endeavor tone, but they have just the right amount of upper mids and treble to them that gives them a bit of air, so given that even if your guitars sounded more "airy"/"fizzy" than the original once you tweak the tones more, it wont be too bad as long as it's not excessive