I have neuropathy and have a lot of trouble with laced shoes. I actually, do a lot better in the summer because I don't have to wear closed shoes.

When I first had symptoms of neuropathy it started in my feet and calves.

Also, I believe that when I am busy I don't think as much about the pain. When I sit down I immediately know it is there. I don't know if this is what you may be going through.

My guess is you have already seen a neurologist. It does sound like you may have done some nerve damage to those toes with those shoes. However, since you are so active it may have happened running. Most of us never know what caused it. If you don't get relief and the neurologist you are seeing doesn't help, see a different one.