You didn't mention that he has actually seen a doctor about his heel pain. He goes to PT on a regular basis (for what? for the heel or something else based on what kind of diagnosis?) What did the chiropractor diagnose?
I agree with Cheryl that it sounds like it could be plantar fasciitis, but I am surprised that a doctor wouldn't have given you a diagnosis of that if that is what it is. Unless he hasn't actually seen a doctor (?).
I had it, and for some people it can be an ongoing very difficult problem to treat. In my case, I did some stretching exercises appropriate to the condition, and rolled the bottom of my foot/heel on a frozen soda can a few times a day and it went away after a few weeks. No more problems for me. Others aren't always so lucky.
ETA after your SWH:
Ok, forget the plantar facisitis, lol.
Obviously, if he has been diagnosed with sever's then you will need to have him follow the recommendations for that condition. May not be what he wants to hear, but from what I read in a super quick search online, he basically needs to stay off of it for some time. It is a growth issue. Normal growth, but in slightly abnormal order. A sort of growing pain issue, that time is the best medicine for.
http://www.orthogate.org/patient-education/child-orthoped...