I've had shoes custom made, well more specifically I had gym shoes custom made that would be appropriate for jogging and xtraining.
The shoe was more narrow that normal cross trainers but built as wide as my foot required, I don't need as much lateral support hence not need shoes as wide but I need shoes to compensate for a pronounced roll from outside of my foot at the heal to my big to.
SOOOO I got shoes custom made, moment i put them on they were the most comfortable shoes I'd ever owned made my Brooks, a model of my foot was sent in along with the specs required and they made the shoe and sent them back.
I warn you though, it's not cheap I paid 17 hundred for them although they lasted me 4 years of intense training, jogging, running around, being an idiot and general stuff and didn't break down until recently.
However it's my understanding that joggers usually break down pretty fast if used regularly so you'd be replacing them every 6 to 8 months so assuming age months and I had them for 4 years it isn't to pricey BUT they certainly cost what a custom pair of shoes would cost.