Thanks Arne, I was hoping you'd chime in!
I know exactly what you're talking about with the uneven shoulders but it's been sort of a "lesser of two evils" thing for me. I have what some might call monkey arms, and I've found that shooting with my shoulders level causes my string arm elbow to be quite high (almost to the 10 o'clock position when viewed from the side). I shot that way for quite some time and I had a pretty significant callous on the bottom of my ring finger to show for it.
I tried the "low shoulder" for about a week and found that my elbow was in a much better position behind the arrow, my release improved and the callous started to fall off due to lack of use. I accepted the imbalance because of the results I was getting but would certainly be open to your suggestions as to how to get better into alignment.
I think just getting the right muscles engaged has been a tremendous improvement from where I started but it's always good to fine tune what you can!