As to factory alignment of the handlebars - there is (according to the manual) a "pinch mark" on the bars that is to be aligned with the rear mating seam of the handlebar clamps. That being said, the more relaxed of a riding position you can achieve, the less pain you will feel. So if moving the bars helps, go for it. Just watch the clearances and the level of the brake reservoir.
The Glucosamine, etc. supplements help, but a lot of times shoulder pain originates in the neck. Just wearing a helmet and pushing through the wind puts a strain on your neck.. If you are tense or stressed that multiplies the effect.
I've had that ice pick in my shoulder pain too, but never from riding my bike. If I'm going on a long ride I take 2 Aleve's before I a-leave....
Aleviates a lot of the aches and pains of sitting in one position for a long time.
