Pain is the real problem. At home he takes a lot of breaks, often lying down when his back hurts...There is no testing accommodation for pain.
Lori,
Since your son has formally diagnosed disabling conditions that include both a significant pain component that is worse with prolonged sitting and a fatigue component, he may actually be eligible for the accommodation of taking the test in short sessions over the course of several days. It sounds like that would be really helpful for him.
When the time comes, it would certainly be worth a try to send in what you have in terms of medical documentation.