Emjae, it sounds like you have a dropped metatarsal head. There are foot exercises to strengthen the muscles that hold the metatarsal arch up. When that arch collapses (cuz the muscles are weak) the nerves that run between the rays get pinched under pressure.

Google "dropped metatarsal head" and "metatarsal arch" and see if you can find a picture of the callous on the bottom of the foot, see if it matches yours. I'm betting yours is under the 2nd or 3rd toe. (the two next to the big toe)

If you do have a dropped met head, you can get met buttons put into your insoles (have a professional do it, they go under the ray, not under the head) that will help you more than a gel insert placed under the dropped head. They will make you more comfortable, and will help to ease the pressure in the met arch.

Then you can do foot exercises to strenthen the intrinsic muscles of the foot to solve the whole issue.