Hi Susan,
first of all let me throw in a little disclaimer: I am not an expert or a pro, so put whatever I say in perspective.
I would strongly recommend 700c. The advantages are enormous - one above all being the endless choice of wheels and tires for 700c. You can find the best wheelsets in this size, both clinchers and tubulars.
The perceived 'issues' with 700's on small frames are really not a deal in my opinion:
The slower acceleration is rarely an issue - as most pro racers can demonstrate, since they race 700's.
People that suggest 650's to avoid toe overlap make me wonder whether they plan to ride in a parking lot at 4mph. Toe overlap is basically never an issue in road riding because 1-we do not usually steer, and 2-we do not ride slowly enough to even encounter that problem. So that is sort of a myth the way I see it.
I would go with 700c wheels, and pick a wheelset you like.
Oh, and by the way - CONGRATS on your custom build!!!