I had really bad inflammation of the right shoulder, which I believe was a result of going from a 70# compound straight to a 65# trad recurve...too big a jump. I was 21 at the time and was the fittest ive been in my life, doing martial arts, rock climbing etc. You have to find a balance between excercise and rest and dtermining your own limits. In my case I simply over extended myself and didnt rest enough.
As the shoulder wasnt getting any better and I couldnt stop shooting (too much fun:) I sold the bow and took a year off archery. After 12 months the shoulder was still painful and eventually I went for a cortisone injection. I hate any kind of invasive therapy but I must say I think it reduced the inflammation enough for the natural healing process to start. Oh yeah and Ive also heard that enough of those cortisone injections and it can actually cause your cartilage to deteriorate prematurely, so Im glad I only had the one!!
But Im back to shooting a bow now, started with a much lower poundage 55#, and now can fling 50 arrows a session with no pain...its awesome!!! I still cross-train as I believe thats imperative to keeping your body in good shape overall, and I dont over do it. If ive had a hard MMA session or workout, I'll fling maybe 10 arrows just to keep my eye in and then give it a day to recover.
As an athletic activity Its almost to be expected your going to pick up an injury along the way, but If you manage it right you'll get back into shooting no probs! But Im afraid to say you may have to cut right back on archery for now until your body heals up. Like the guys have said see your doctor and get a good rehab programme going now, before you over do it and it it takes a year to recover instead of a month.
Good luck Bakes, let us know how you progress.