I don't know if this will help, but I have a Morton's neuroma on the ball of my right foot that has caused me a lot of pain and numbness when running and cycling. I used to wear thick socks when I ran and my cycling shoes had a narrow toe box. I switched to thin cycling socks for running, and bought some Sidi Genius 5's that have a larger toe box than my previous cycling shoes, and that combination seems to have cured the pain and numbness. Having room for my forefoot to spread out appears to be the key.

Good luck.