Tommy - there are alot of possible explanations for the shoulder pain... I agree, you may want to consider an MRI if the pain persists much longer, just to be on the very safe side... sometimes pain starts off slow and gets gradually worse....
As for anti-inflammatories, I used to have a PT tell me to take 2 alleve several times a day... there are those that say NSAIDs are not good for you (also hinders muscle growth). I personally take more natural anti-inflammtory supplements like EFA's, krill oil, CMO, etc. Glucosamine and gelatin are good to throw in for the joints, but they take several months to show any benefits.
Definitely do the stretches and exercises!!!! 2-3 times a day (and right before every workout)... 5-10 minutes... you should ice after doing stretches... and after your workout... ice brings down inflammation
Sleeping the "wrong way" on your shoulders will definitely cause pain - try changing your sleeping position if possible. Also, if you're sitting at a desk all day long staring at a computer screen, that could contribute to upper back / shoulder / neck pain. (Stretch throughout the day!)
Another thing I noticed with my shoulder pain is that most of the pain was actually being caused by severe knots in my upper back as well as a tightening of my c-spine... for whatever reason, the pain seemed to come from the shoulders instead.... I've been seeing a good chiropractor for that, doing stretches + icing several times a day and it's gotten much better
Finally, you could just be going through "growing pains" - I've heard it said before.... you cycle and you grow, sometimes way too quickly, and your body responds with pain.... just keep limber/stretched, take the right supplements... you should be ok