Rotator cuff problems are common in the swimming world. You may find as I did, the problem is not the reach out of the water, it is the pull underwater. The way to ease the pressure on the rotator cuff is to make your pull underwater shallower; bend the elbow and pull your hand along closer under your body. Don't forget to stretch the shoulder after you are completely warmed up.
To work on breathing, use a leg float and just do an arm pull and try concentrating on alternating your breathing on each side.
+1 on Bending your elbow through the stroke. Here's one way to think about it. Your entire arm is the "paddle" pulling you through the water, not just your hand. The entire undersurface of your arm sould be pussing water. This also happens to keep your sholder straight out. Also, you're correct that if you are breathing to your right, you may be reaching accross your central axis with your left arm. THis way my major problem in 4 years of college swimming.