First, if you and your son are testing very low Total IgA than none of the IgA based antibody tests in the celiac panel will be accurate. Request a written or electronic copy of what tests were run for both of you. The IgG based antibody tests are essential with low Total IgA and there should be a Total IgG run as well - which is rare for doctors to order, because it is possible to have low Total IgG as well - which would make the entire celiac panel inaccurate for you.
Is the doctor that suggested the return to gluten based on a lower Total IgA the same doctor that conducted your endoscopy? The reason I ask is his advice to return to gluten ingestion is bad advice and I wonder if he was qualified to accurately conduct your endoscopic biopsies. It would be wise to request a copy of all medical tests, including endoscopy.
It is not uncommon to have improved symptoms when newly gluten free and to have either some symptoms return or worsen in severity. I do not agree with the "placebo" comment given your reference to Fibromyalgia.
It is also common to become intolerant of other groups of foods while your digestive system is healing. Dairy, Grains, Legumes, Nuts, Seeds and Nightshades can be problematic for different folks - often these intolerances are temporary and once the gut is completely healed they return to eating them with no problems.
I suggest you remove all gluten again and start a food/symptom log - keeping track of symptoms is important because some reactions are not immediate and looking back over the three days before symptoms appeared can be helpful.
Given your "fibro" symptoms, I also suggest you try removing the nightshade group - tomato, potato (sweet potato/yams are ok to eat), all peppers (black pepper/corns are ok - but no pepper spices, paprika, bell peppers, etc) and eggplant as many folks with muscle/joint pain find relief when this group is removed.
The road to healing is not always as simple as remove gluten and you are fine - despite prevailing medical theory that all we have to do is remove gluten to heal -- especially in cases where there is many years of damage from undiagnosed Celiac Disease.
Hang in there....trust your gut