I believe the Project 1 is Trek's version of Burger King - you can have it your way, right down to the paint scheme. I've never been in the market for one so I don't know how far they take it, but I'm pretty sure you can spec every component on it (if you want). Someone considering one of these is going to need a lot of assistance from the LBS, not necessarily in deciding what pieces and parts, but certainly in going over all the options available.

OP - Glad to hear you have at least one good LBS who is deserving of your business. Can't wait to see the pics.