I picked up my first road bike in September and still have shoulder and neck pain after anything longer than an hour. Last week my friend told me about keeping my elbows in. I have a tendency to kind of wing them out. On the 50 miler Sunday I made a concerted effort to keep my elbows in and I noticed a big difference. Sure I was sore, but it was definitely better than past rides. Perhaps you're unknowingly doing the same thing?