It's great that you've been to your doctor to get things checked out. I'm not a doctor - so can't begin to give you advice on what to do or even make a guess at why it's like that. Even though your x-rays and MRI didn't find anything...did you ask your physician if it was anything to be concerned about, or if there are options to do anything for it???
I'm always open to the possibility that exercise might make things more even, and Pilates training would be excellent for getting good mobility through the spine and ribcage. Chances are there's some scar tissue around the ribs that were injured, and breathing habits may have been altered since when the ribs hurt chances are there was no deep breathing going on.
There's a great Breathing article on my website
http://www.CenterworksPilates.com with some easy things you can do at home that might be helpful. Always good to touch base with your Dr. before doing anything new, especially since it's post-injury.
Hope this helps!