When I began to ride I had the same issue. I had a professional bike fit, and still experienced shoulder pain. I do yoga, and remembered that we were always told to keep our shoulders below our ears. I agree with the statement "Consciously work on bringing your shoulders into a level, neutral, relaxed position." I don't really know if this is why the aching stopped, or if it was just a matter of getting into shape, but I no longer have the same problem. Wish I could share more, just wanted to let you know there is a possibility it will go away with time.