I've worn custom orthotic innersoles (from a podiatrist) for nearly 3 years now. After going through a series of injections for neuromas in both feet, the orthotics keep the pain from returning. I must wear them all the time; they last about 1.5 years. Because I have high arches, the neuroma-fixing orthotics mean that I can no longer wear any shoe that doesn't have laces and a high enough toe box. So I understand your dilemma! $350 for a pair isn't cheap, but worth it if it means I can sleep at night.
I looked into custom shoes—not to help my pain, but to allow me to wear nice-looking shoes that accommodated my orthotics. Most custom shoes are around $700-800; a significant investment. Of course, these shoes can be resoled repeatedly, unlike most modern shoes. So over a long period of time, the price drops. The shoemaker will take all your measurements and go through detailed questions; some will make a mold of your feet (with and perhaps without any orthotics). So, you either need to find someone local or you need to coordinate a fitting. I was fit at a craft fair where the shoemaker had a booth.
I haven't decided if the custom shoes are worth it. However, I only have 1 pair of really comfortable shoes right now, and I'm about to begin a search for new ones. The unfortunate trend in footwear, including athletic footwear, is non-removable innersoles. If the innersoles don't come out, I can't put in my orthotics (stacking them is a bad idea, and my foot wouldn't fit, anyway). So frustrating. And endlessly time-consuming!
I have heard about a local (well, within a few hour's drive) shop that specializes in challenging foot problems and yet has somewhat stylish shoes (often from Europe). Perhaps you can find such a store near you? The one I'm talking about is at waxbergs.com. The can alter shoes, too. And if that isn't enough, you might want to find a certified pedorthist. They specialize in this.
Good luck!