I just bought a Trek5000 WSD and it came in Iris blue (the LBS was calling the pink color - that pepto bismol bike...) I shopped around - this LBS would swap anything out for me for very little extra cost. It came with a triple crankset which I had them swap for a ultegra double compact50/36 for $20. (and then swapped out the cassette and shifters) I test rode the triples and didn't like the way they shifted. I upgraded my wheelset, also-- I got the Bontrager racelites for $150 (I really like them!! woo hoo) When they fit the bike, they put on a different stem (I have short arms) for free. I am very happy with the WSD shifters and brakes - I can reach everything - I have small hands. I couldn't even reach the brakes on the drops of my Specialized.

Anyway, I'm happy with the WSD and the LBS. (Most of the shops I checked with would have charged me full price for all the upgrades). It wasn't a totally custom bike, but it was close and for a price that was close to the original price. Ask for free stuff - they should throw in a pair of cages, install your computer, your light, etc.