I owned a 2006 Madone 5.2 with Ultegra (including crankset) and Race Lite wheels. I got a better deal on the 2006 v 2007 but always regretted not getting the 2007 Madone 5.5.
My 2006 was fabulous and I enjoyed it. The Race Lite wheels that were on the bike were BS but okay. I am not sure about the reliability of the Bontrager Crankset and it may be heavier. I seem to recall problems. Make sure you are getting Race X lite wheels. They are about 400 gms lighter than the Race Lite.
However, at that price point, you can almost have the pick of the litter. I would check out some other bikes since I think that is part of the fun of getting a new one.