Will your frame be steel or ti or something else? Custom steel forks are nice and can provide fender clearance if that is an option from your builder.

I had a custom road/commute/touring bike built two year ago in steel. I'm 5'7" with a 32 inch inseam and went with 650. Actually, I let the builder pick the optimum wheel size (though he was on the fence until I told him my shoe size). I'd rather have perfect frame geometry than a compromise to fit a pre-determined wheel size. And the feel and handling of this bike makes it worth it. At the builder's suggestion, I have two wheelsets, 650c and 26". I run 650x23 tires on one wheelset and 26x1.3" (sometimes 26x1.5") tires on the other. That's one way to get a wide choice of tires. The brake pads have to be moved by 3-4 mm when I switch wheels. As it turns out, I love the feel and versatility of the 26x1.3" tires so much that I ride them most of the time. I run full fenders most of the time also.