Man... both shoulders, that sucks. I'm in the same boat. Your problem is likely either structural (connective tissue, bone, etc.) or mechanical (improper firing muscles sequence, compensation, or muscle imbalance). The pain will probably subside with rest, but the underlying cause of the pain won't. If it were me, and you ain't me but this is where I wound up after 4 years of pain, I would go to chek institute and find a level II or III practitioner in your area. They should be able to identify bad movement patterns in your shoulder and refer you to a specialist if needed.
If nothign else I would call and ask the practitioner for the name of the best shoulder therapist around for an evaluation (CHEK practitioners usually have a network of specialists (the best) that they recommend). It's better than pot luck anyway. Good luck to you man.