Spend the money on the better frame (assuming that you've tried it, you like it and it fits!) before you spend the money on top end components. You can always upgrade later.
From what I've seen, the price difference between Ultegra and Dura-Ace has been closing.
Another option is to go with Dura-Ace derailleurs with an Ultegra cassette (and keep your FSA crank - IMHO the SLK MegaEXO is a great crank). I've seen quite a few bikes being spec'd this way now to keep cost down but still provide the shifting quality of a Dura-Ace derailleur.
(e.g. Cervelo -
http://www.cervelo.com/bikes.aspx)
As far as I know, the only real difference between the cassettes is weight. I think many pros train with an Ultegra cassette because it's a little more durable (they log a lot of miles!) and switch to the Dura-Ace for racing.
One other consideration - if you can find a bike you like factory spec'd - it will almost always be cheaper than buying a frame and building up a bike! The only people that I know that go the build route are super picky or have money to burn (not me)!
My $0.02