I have no idea what's wrong with my feet. Can you help me out?

It started at the tendons at my toes, and I got that from our coaches severely over training us in our distance running. The injury occurred in the middle of April, and at first we thought it was a stress fracture. It should be healed by now, and I haven't done any running at all, but now the injury is in both my feet and is now in my arches and achilles tendons. I went to physical therapy, but all they did was give me foot pads and told me not to run any more. The pain has gotten worse. What could be wrong?