Thanks for the input guys!
A lot of the problems you've mentioned are things I really like bout the mix, so I guess it's good these aspects are noticeable!
The weird crackle is the organ driving a delay pedal too hard, we noticed it right away but really liked the take so we kept it.
Not sure what the out of tune guitar is, I'll have to check that out.
There is an acoustic 12 string that comes in with the unison strings de-tuned a bit, and a guitar with pitch vibrato.
Also, are you saying that the drums and guitar are the dark parts of the song?
I was actually a little concerned the drums were too bright (for my taste!).
I was also a little concerned how people would feel about the bass and kick as I really am not a low bass kind of guy and roll things off from 100 frequently!
Also the drums on this song we're recorded with one mic.