I might be a little suspect of your LBS, if they are pushing what they have on the floor over what you seem to be leaning toward. So it you are thinking of custom, you might want to find a better LBS.

That said I'm not sure how close you are to Portland, but they just hosted the hand built bike show. Looked like many local builders were present. I think I would ask around for a great LBS that specializes in custom bikes. It might even be worth taking a long weekend trip to Portland to check them out.

I'm still sold on the Madone. If I ever go custom, I would likely go TI. There are more builders doing carbon, but if you really want a carbon bike, I still think Trek might be the way to go.

Good Luck and have fun with the process.