Not sure if this test is done in the US, but you might ask your gastro about it - calprotectin stool assay test. Non invasive and cheap. If the calprotectin level is out of range (norm is 20, mine has been as high as 80), this shows inflammation somewhere in the GI tract. If high, the gastro can then go ahead with other invasive testing to rule out Crohn's, ulcerative colitis and coeliac. I have Crohn's and have this test done regularly.
Children as young as 6 yrs are now being diagnosed with IBD, and this could be the cause. Hope you get a diagnosis soon and your young son gets appropriate treatment.
Liz.
My son is now 34 years old and was finally diagnosed with Crohn's disease in 7th grade when his blood count was so low they thought he had leukemia. He had symptoms like your son's for 2 previous years, even had surgery for anal fissures and skin tags. I had him to the emergency rooms so many time I can't even remember. Finally I found a great internists that looked at the same x-rays as others and said I think he has Crohn's disease by the ileum. He was correct. Don't know if this will help - but the pain was so intolerable. Let me know if I can answer any of your questions.