What Causes Soreness In Upper Arm And Muscle Below Shoulder Blade?

I have a 17 year old son who has played baseball since he was 5 years old. He is a left handed pitcher who has developed soreness in the side of his upper left arm and the muscle below his left shoulder blade. We had him rest for two months, but when he started throwing again his arm hurt. We went to his regular doctor and he recommended physical therapy. He did a series of exercises but no improvement. We saw a chiropractor and they massaged and tried heat and electronic stimulation with a little improvement. The trainer at school thinks he has two knots in the two areas and it is a very slow, long process. Not sure what to do except for looking for either a sports medicine or orthopedic doctor. We appreciate any advise you may have.