if you feet are relatively normal but it is a leg length discrepancy only I would go see a reputable fitter. I've seen shims for road pedals to correct leg length discrepancy.

I would look to see what can be done buy a good fit before shelling out for a completely custom shoe.We're Bike Fit Experts! (Get that bike fitting done right!) - Alter Ego Sports :: Winnipeg, Manitoba Canada

you could also work with them to see if an orthodic would work.