Shoulder pain could mean a few things: You're bending one arm far more than the other; One arm is longer than the other; Your posture/sitting causes you to lean too far forwards when you ride, putting a lot of strain on the forearms, hands, and, of course, shoulders.

You could try fiddling with the seat angle (bringing the front upwards a bit) or handlebars (adjust for a longer arm by adjust the height or angle).