The repetitive actions involved in casting during fly fishing can create trigger points in the muscles of your shoulder girdle, particularly infrapsinatus, supraspinatus, deltoid, and the middle fibers of the trapezius, that can create the feeling of joint pain right in the shoulder itself. The "on and off" nature of the injury makes it sound like it is not acute (strain, partial thickness tear, etc...), but it should be looked at.
If you are interested in going a natural route, a chiropractor can easily manage your shoulder. They are well trained in dealing with these trigger points, as well as any other possible pathology you might have there, whether sprain, strain, tear, etc... They can figure out what it is and get you healing and back to fishing without any intrusive surgery or medication. Good luck!