I can't speak to your neuroma, but when I get foot and leg cramps, it's typically because of form/fit issues. I had my saddle way too far forward earlier this year, and was ankling quite a bit. When I moved my saddle back and started trying to concentrate on pushing through my heels, the cramps went away. Although I was getting it in the big toes and up the foot through the shin... so it may have no relation to the trouble you're having.

Hope you get it worked out though