Some of your pain might be caused by trigger points in the muscles. A lot of the shoulder trigger points refer pain into the joints.
Have you considered seeing a massage therapist who is qualified in Trigger Point Therapy?
quite often when you injure a muscle it develops trigger points as a result of the inflammation from the original injury. And they can persist for a very long time after the injury has healed.
I have successfully treated huge numbers of people for shoulder pain by treating their triggerpoints....
The fact that you say it is in the scapular area makes me wonder if your Subscapularis is bothered...
Beyond that, if it was a muscular injury, upping your protein intake won't hurt.
But I would try the massage therapy as well.