I can't believe that his doctor hasn't suggested he be tested for Celiac disease or a severe gluten intolerance. Not saying that this is the answer, but it was for MY child who was in constant pain.
Heads up...do not change his diet. Have him tested. Simple blood test, if the results come back suspicious, they'll do a biopsy for confirmation. If you take him off a gluten diet before testing, it can skew the results. It's a simple blood draw, and results can be had within days...very important to keep feeding him everything you do now to diagnose this condition.
I'll just say that removing gluten from my daughter's diet was like a miracle. All of a sudden, the hourS long fits were over. The thrashing and screaming was over. She began growing, teething, walking, eating, talking, smiling, laughing. Her CRAZY skin conditions cleared up.
Symptomatically, is he often constipated or have diarrhea? Does he have any skin conditions? Does he have a hard time gaining weight? All these also might point to CD.
And yes, the pain with CD IS severe. At least it can be...I have a living, breathing child in my home with CD and her pain was obviously excruciating.
(Also, I have kidney stones. I've had two pass in my life and that pain is excruciating beyond belief...think childbirth...but this isn't a chronic condition. Within two days it's over...and hurts that bad until it is.)