I have a 2007 Madone 5.2 with Ultegra $2.8K out the door no pedals. The only parts that are Bontrager are the saddle, seat post, fork, and wheels. It is the best bike I have ever ridden.
It sounds like the $3.5K may be last 2008 summer's price, so it would seem like it can still be discounted some for summer 2009 closeout. From reading those reviews, it looks like there may be some problems with some of the components which can probably be switched out for the same price of $3.5K. Maybe change out the crank set if there are problems with Bontrager.