I went through the same thing as well a few months back to a lesser degree. Turns out it was from bad form while benching. I was lifting my left shoulder to assist on heavy weights--arching my back and using my shoulder to leverage upward instead of keeping the shoulder blades flat on the bench. So my advice would be to check your form next time you're in the gym and see if you are doing something like this.
For rehab execises, gently work the supraspinatus muscle (a band that runs underneath the deltoid and is used for switching the load between anterior, medial, and posterior). There is a good workout called "Triple Decker Delts" that discusses how to hit the supraspinatus.