to discomfort looks liek you're havign a hard time getting your hip drive when it's heavy, that's pretty common but you could try moving the feet out a little to see if you get better hip drive.
there is no "should" in my mind WRT to low bar vs. high bar. Rippatoe's baseline squat stance is a very neutral, mid-width stance and it works for a pretty much everybody. You appear to have longish legs and what's more, long femurs. If you are going to run a lower bar style squat, you might need to go a little wider to feel comfortable, I don't mean double ply squat gear wide, just slightly wider than you are now. if the upper back bar positon is working for you just play with the foot postion a little, try some box squats to a low box (below parrallel) but no where near as low as you're going now) to find if a wider stance will work for you...if not no big deal.
I too have screwy geometry for squatting and am just used to a narrower stance like you are running.