I really don't know why your arm is hurting that high up. Maybe your stance is a little off and you're pulling the bow over to line up on the target instead of being in natural alignment? Maybe you should check with the doc.

A few exercises... with weights: Upright rows, lat pulls,reverse butterflies; using body weight: pushups, pullups, crunches, shoulder rolls, windmills. Swimming. The basic crawl stroke and the breast stroke are good exercises to strengthen your shoulder muscles.