Hi Christine,
I've never heard of using road shoes and cleats to increase standover height -- did the LBS guys tell you that? Road shoes with cleats, while providing a very stable platform when clipped in, are anything but stable on the ground. Unless you get expert advice that road shoes will really help in your situation, I'd be kinda sceptical.
I have an awful time finding shoes that fit too, and am hoping someone comes along with an answer. My feet are wide (but big) and over a size different between left and right. I've had moderately good luck with Diadora's, which are also reasonably priced. Other good brands are Shimano, Nike, Lake, Pearl Izumi, Sidi. Really nice shoes will set you back almost $200 dollars, though, so I'd have to assume custom shoes would be astronomical. REI, Performance, and your local bike shops should have shoes to try on.
Now I have to climb on my soapbox for a moment. I really think road shoes and cleats are inappropriate for beginning riders unless they plan to race. Actually, I think that for most "enthusiast" riders who want to tour, walk into bathrooms, or walk into convenience stores, all without falling, mountain shoes with recessed cleats are the best solution. Okay, I'll step down from the soapbox now.