Go back to the lbs and tell them of your discomfort, etc. A reputable shop will make it work. Not knowing what size your bike is, is wrong, wrong, wrong. Especially after paying for a fitting. It all, bike size/sizing, parts(stem, handlebars, etc) and your measurements, should have been explained to you as well as a written copy of all the measurements.

On the other side. It may not be correct that your friends bike must be the right size because "it feels more comfortable". It could be that your body is just acclimated to that size and fit which translates to more comfortable while in fact it may not be "correct" for your body. It may be the right size...but that is impossible to determine via this post.

East Providence Cycle used to, I don't live in the area anymore and don't know any of the people there, have a very good reputation for customer service. Perhaps try them as a secondary source...unless that is where you went...
What fit system did they use to fit you? They should have told you what system they are using, for your knowledge, as there are a few out there.

Good luck and keep us informed.