Get your upper back off the top of the bench. This allows the scapula to move with more range of motion, allowing the pecs to get into a more lengthened state.
Keep your palms forward and bring the dumbbells back toward your ears, not down to the side of the body. This also puts the pecs into a deeper stretch.
Use only a slight bend in the elbows. Most people get way too much fixed elbow flexion with flyes, turning into more of a half press/half-flye type of movement.
Dr. Ken Kinakin, much like Dr. Mike Leahy, knows your pain. In fact, he's made a living off of it. The doc is one of the best in the world at devising training protocols to help make you injury-proof. Yeah, he likes bodybuilding and powerlifting routines, too, but when it comes to figuring out how to fix what ails ya', he's one of the best.