I'd think buy the bike at Performance, spend the extra $200 at the LBS and everyone will be happy. It's my understanding that LBS margin is lower on bikes than anything else they offer. Plus, you get more goodies that way.

The 49cm Fuji looks like it has very similar geometry to the 47cm Canndondale (same effective top tube length, etc.) so I would expect that it could be adjusted to fit you nicely.