The only "normal" pain that I know of for bike riding is in the lower back due to what the position of riding does to hip flexors. That, however, should be less of a problem for most tourers due to a more upright sitting position. My guess with shoulder pain is probably a bad fit and perhaps poor posture that requires a lot of pressure on the shoulders to hold up the torso. You can find lots of good resources regarding bike fit on the net and see if you are in the ballpark.