AYYA wear <-- These folks might be of interest to you. I stumbled across them looking for tabi shoes; they appear to make custom footwear for reasonable prices (reasonable, of course, for custom work... which isn't cheap, but they're not charging hideous prices FOR custom work). I can't speak to the craftsmanship or longevity, personally, but I was planning to buy a pair of their tabi shoes as a pair of 'barefoot' shoes so I suppose when i get around to that and get them I can let you know what I make of them.

Anyhow, they say they'll make shoes to order based on your measurements; if your feet are actually of different sizes, they'll apparently happily make you different sized shoes.