I have been dealing with a similar issue since high school. Got tendinitis pitching my junior year and been dealing with it for a while. my right shoulder pops and cracks with any overhead movement and deep bench presses cause extreme pain. I did tons rehab/mri/corta shots and the only thing that worked well/cheap and practical imo was MSM/Glucosamine/Codroitin pills and these exercises,
try doing these as a warm up next time you do any kind of shoulder/chest movement.
http://videos.bodybuilding.com/video...maleshort-clip
http://www.youtube.com/watch?v=eQ0qxpEXfbM
-i usually do them standing but sitting helps to get the movement down at first, do 10-20lbs 10-15 reps 2x each alternating