Dura Ace should not be so finicky and require such regular adjustment. It is really hard to tell what/where the issue(s) are, but I would definitely consider another shop. It makes no sense to do some of the maintenance procedures they have done, given the issues you describe (like why would you need to replace the bottom bracket??), and Dura Ace should be more durable and able to handle plenty of miles without going out of adjustment.

Also, a lot of stock bikes, even (sometimes especially) carbon bikes can have alignment issues that could be contributing to your problems (like chainline). It might be worth having a qualified mechanic check alignment, if he can (most shops don't even have the equipment to do this). They usually can and should check the frame's derailleur hanger alignment as that can cause the problems you are describing.

Anyway, my 2 cents is find a very professional shop that has no relationship with your other one, and start there. You're in Denver--there are some good ones! (Wheatridge Cyclery is coming to mind...). If you're in Boulder, Vecchio's has one of the best mechanics around (Peter).

good luck-