Hey!
I agree with gymdandee; also would like to add that once you are normal again, please change the shoes you are using at present. May be you are using a wrong type of shoe that is not co-calibrated to your 'foot-type' - if you have access to a sports-physio store or a fitness expert, please get your foot-type checked and get a new pair of running-shoes accordingly.
All the best,
Parth Adhyaru
http://www.bodyweightworkoutsystem.com/
sounds like you have Neuroma A neuroma is a thickening of nerve tissue that may develop in various parts of the body. The most common neuroma in the foot is a Morton’s neuroma, which occurs between the third and fourth toes. It is sometimes referred to as an intermetatarsal neuroma. “Intermetatarsal” describes its location in the ball of the foot between the metatarsal bones. Neuromas may also occur in other locations in the foot.
You probably should get a Cortisone shot and maybe Orthotics. see a Orthopedist or a Podiatrist.