Welcome rdreher1976.
As you can tell from my signature I have CMT (Charcot-Marie-Tooth Syndrome). I assume that is what your son has from the subject. There is at least one more person on here who also has it. There are many types of it as you may know.
Does anyone else in the family have CMT or symptoms such as your son? You could talk to his neurologist or AFO person as to what might help. Perhaps he needs a different set of AfO's. But it seems legs and feet hurt regardless if on them a lot.