A. It's hard (if not downright impossible) to diagnose the cause of shoulder pain over the internet.
B. There's almost no such thing as a "wrong" bike for commuting. Back when I raced, I rode my race bike (since is was my ONLY bike) for everything. Commuting to work, errands, everything. I never had a problem with it, and it was as racy as anything of it's time.
C. Go see a doctor and have him figure out what's causing your pain.
D. There has to be a good bike shop in Austin. Find it. Get a fitting.