That said, it is indeed possible to buy custom running shoes. For a price, of course. The Hersey Custom Shoe Company in Wilton, Maine, makes several running shoes, among them the Original and the Custom DPS. They're not the most high-tech-looking shoes on the market, but they're extremely well-made and use high-quality materials. They are not throwaway shoes—you can have them re-soled several times before they head to that Great Shoe Store in the Sky.
Hersey's website (www.herseycustomshoe.com) offers detailed instructions for making a pattern they can use. Basically, you need to make a tracing of your foot and mark any abnormalities such as corns. They'll then make a last (a form on which the shoe is built) to make the shoe of your choice. It isn't a cheap process: the charge for making the last is $150 (although that's a one-time expense). The shoes run between $200 to $250 depending on the model, and several options could boost the per-shoe price to almost $300.
Hersey shoes may be the solution to your problems. But...I'd still see a foot doc first.
Discover of world of running-shoe comfort in Outside's 2004 Buyer's Guide .