well, let's dispense with the fork problem right off since you're getting a custom bike. Get the custom fork that your builder is so proud of and you'll do fine.

I went with the 700 wheels myself when faced with the same dilemma and honestly, i wish i had the 650's when i see how nice they look.
i have friends with 650's and have been told that they don't feel like they are working any harder than they did before.

however, my husband who has 700's was kind of strong in wishing that we had the same kinds of tires (which also eliminated the terry with it's odd front wheel)

Next time i'm getting a 650