and the truth of the matter is that even great bike shops don't always deliver the bike you wanted.
in some ways, by going custom, you stand a greater chance of it not being exactly what was planned.
my husband had chroming done on his bike. It went back to the chrome shop 3 times. In the end, he did not get what he asked for.
Another person i know wanted plenty of fender clearance for his tandem. frame came back with enough room for 25mm tires and fenders, but no bigger. They were pretty upset.

good luck.
oh, and they are never done when they say they'll be!