Definitely check the prices. I built my all carbon Cannondale Synapse from the frame up and it ended up being a little bit cheaper than getting one out of the box. The frame was a 2008, never built, brand new one, sitting around at their factory that my LBS special ordered for me. And I helped my mechanic put the bike together so I didn't get any labor charges. A 2011 Synapse Ultegra will run you about 3100, but it doesn't have carbon handlebars, seat post or good wheels. For the 3100 I got the box bike plus better wheels (mavic ksyrium elite) and zipp bars/seat post in carbon.

Hang around your LBS. They are pretty willing to work with people they know. I'm pretty sure buying pizza for everyone on the day of my bike build helped too