I had some nagging pain a couple years ago. I think it started with a rough day of playboating, but it took forever to go away. The thing that I found helped the most was probably backpaddling to build rotator cuff strength. I'd say 50-100 backstrokes at some point during your paddling day would help a lot.
My wife also had some shoulder pain, and hers was due to an impingement if I remember right. She had developed a muscle imbalance where the front part of her shoulder was stronger than the back part, or vice versa, and this pinched a nerve or something, or held her shoulder in a painful position a lot of the time. It was a while ago, and I can't remember the details. She saw a doctor and got a list of the specific shoulder exercises to strengthen the weaker parts of her shoulder. Once she did that, her problems cleared up a lot faster than mine had.