Good point about the rotator cuff. My issue was rotator related as well.
Twice a week I did these three exercises described on this site:
I used light weights (2.5lbs - 15lbs) and high reps (12-15).
Also I started putting some ephasis on rear delt strength. I started with reverse pec deck flys and then eventually graduated to face pulls.
This seemed to really help my issue, along with avoiding any movement that hurt.