I'm in Berkeley as well - very, very happy with Cyclesports on Grand in Oakland. Talk to Chris Blease, the manager, and tell him Aaron sent you over. They have great service, carry trek's and generally really good to do business with. They also do a lot to support th local bike teams/clubs - lot's of community involvement.

You might also try Left Cast Cyclery on Dominguez - smaller shop but thier wrench has a great reputation. They carry Treks as well. Skip Wrench Science, only very high-end custom frames.

Edited to add - Quality fitting is the critical element, and one that both Cyclesports and Left Coast will excel at.