Wow, where do I start. I have a 13 year old boy with Duchenne Muscular Dystrophy, DMD, and we went through all sorts of fun when it came to potty training. I think he was finally potty trained right before he hit kindergarten, but he still had accidents here and there at school and he wet the bed often.
Most parents don't even think about letting their kids know what is going on with their bodies in this type of situation, but you've got to tell him something. He knows, believe it or not, that there is something going on with his body. You've already got a great start, we go to Children's Hospital for Muscle clinic and they are a very knowledgable group. They've been there for my family. You need to tell him somethings about this disease as it will affect him more than you.
Second, DMD is a muscle wasting disease and you don't realize how much of your body is muscle and how much muscle weakness affects alot. Like pooping. We had issues to where my son wouldn't poop in the potty at all. He would go in his pants while nobody was around him. It was alot of work, but I would take him in to the potty once an hour until it finally worked.
The DMD docs are great, but they are not the answer to every problem. Your primary pediatrician or family doc can be of more help with the pooping thing as well. It could be as simple as he hurt his butt pooping one time and now he's afraid or it could be his way of acting out because he feels something going on but nobody is telling him anything.
My son was diagnosed at 9 months, when he turned 4 we told him that he had this disease that affected his muscles. We went through alot and I didn't want this to turn into a book. If you'd like to write me, let me know and I'll get you my email address.
Just know that you should probably talk to your pediatrician, they could have better answers than everyone else.
R.