Shoulder and left flank pain
With the usual disclaimers that I'm not a doctor, etc, it sounds like you strained an intercostal muscle when you hit the pothole.  Intercostal muscles are the muscles between your ribs; they assist in breathing, which explains why you experience pain with deep breaths.  As with any muscle strain, the only cure is time and resting the muscle.  Wrapping your chest with an elastic bandage might help.  Consulting the sports doctor would be better than asking me, but my bet is he'll tell you the same thing.

But to answer your actual bike question, I don't think it has anything to do with bike fit.  It's a physical injury.