Sounds like a neuroma and/or the beginnings of a hammer toe. I have one and had the exact symptoms you describe. My ortho specialist said contributing factors are shoes that are too small and/or narrow in the toe box, thus making your foot scrunch in the middle, along with shoes/boots with inflexible soles, standing too often (pressure) and possibly other health problems that might contribute.

He prescribed some orthotics, said the hammer toe "is how it's going to be" for now -- could get worse over time, thus requiring surgery -- and for now for me to use the orthotics, get shoes with a wider toe box and possibly a half- to full-size larger for better foot expansion.

I've done all that along with dropping about 30 pounds, stretching and doing yoga, and it has helped. My foot pain is gone. I'm currently wearing Altra Lone Peak 3.0 shoes and will be transitioning my other jogging-running-workout shoes to them. They're great (for me).

See a specialist. I see this specialist at TOC in Huntsville and have been quite pleased. He played football at Duke and is considered one of the best foot specialists around.