I think you are freaking out. I put myslef through college on a swimming scholarship and I still have trouble with my shoulder. Last year went back to the sports med dr and got some therapy exercises. If I start hurting again, I just do the exercises. It may be worth your time to see a PT.
Also, I know how you feel.....I think this disease has made me so much more aware of my body to the point that I now feel like a hypocondriac. But, I really do think it is just an overuse problem, and it will clear up with a little rest, and possibly some strength exercises.