You are in luck my friend as i have the exact same problem.... actually you arent in luck. When i run also, my feet hurt on the arch (left, right, or both feet) and sometimes the area by my big toe on the right foot hurts. Just like you, i feel a burning or someimtes a sharp pain in my feet after/during a run.
I have two problems with my feet 1) they are flat (low arch) and 2) i have a bunion on my right foot.
The low arch can't really be corrected; it can only be prevented from worsening by the use of orthodics (special soles for the shoe with high arches).
The bunion (which is when the joint for the big toe sticks outward due to a bone overgrowth) i had surgery on, but it didnt really fix it and it still hurts. I dont know if you have a bunion or not, but i know that for me pain around the big toe is from my bunion.
There really isnt much of a remedy for flat feet and a bunion. You would know if you had a bunion because the joint visibly sticks out... so i think its most likely that you have flat feet. You said you did something to you ankle, but after that's healed i dont know how it would cause your foot to hurt. Orthodics help but there's no real solution. A few years ago, on doctor recommendation, i took advil daily to relieve the pain. Well, after a year of daily advil use i became nearly immune to the stuff, and now i have problems with acid in my stomach. So however you try to cope with your feet, dont get into the habit of just taking pain medication whenever you run.
Hope this helps you but i really dont know exactly what you have. Please post a response to this!
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