I have a pair of custom orthotics that I use in my cycling shoes. I had to pay extra to get the second pair made that would be narrower than my running shoes. The custom orthotics make my shoe feel soooooo much more comfortable but I never had pain while riding only while walking/jogging.

if your insurance doesn't cover custom orthotics, then try getting BFOs. (Or your podiatrist may have them. My podiatrist gave me these temporarily until I got the custom orthotics. They cost $20 total and were very comfortable.)