I love that LBS that you go to and recommend everyone go there. With that being said, you pay what you get for. If you get it through that LBS at least you know you'll be getting the best bike possible. Obviously it'll be way cheaper if you did it yourself (I built my computer and saved 500 dollars doing so) but it's a risk you have to wonder if you're willing to take it. I recently went to that same LBS to inquire about custom wheels and yeah they are expensive but they are gonna build those custom wheels for you with the best parts around. At the moment I'm wondering if I should get custom wheels as my rear wheel bombed from a Flatbush pothole but Velomine has them for way cheaper. If I were in your position (which I kind of am as I am planning to save cash for the 725) I'd totally neglect the carbon fork and custom wheels and you'd save a ****load more.
If there's one thing that's certain from my experience with that LBS is that they will NOT rip you off. They didn't win an award from New Yorker for nothin. Check my review of them under my name here on Yelp for a better idea on my experiences with them.
I'd bring up your concerns with them as they actually are real down to earth. You'd be surprised at how honest they are.