Hi! How is your son doing? I am thinking i will do a post on this forum. I believe i know a possible reason to his pain. Please read this post.
http://www.medhelp.org/posts/Thyroid/Rice-Krispie-joints-to-Jimlow/show/262869
I have joints that make cracking sounds and hurt. It goes away when i dont eat yeast, MSG(made with yeast), vinager(made with yeast), most b-vitamins(yeast), grains, smoked meats or fish(mold spores), fish that has been fed grains, and to some degree also milk. If i eat it, my joints start cracking after one hour. I have researched and it can be an overgrowth of an intestinal yeast called candida that is responcible for the "allergic" reaction.
Hope you test cutting the things out of his diet and see what happens.
Best Wishes, Sandra