IBD/IBS/food allergies are very specific to each individual. Based on his history, I would guess he has IBS (irritable bowl syndrome) or food allergies (which technically could fall under the IBS umbrella) The treatments for all three are pretty much the same, most important being finding a food they do well on! Food allergies/sensitivities often can change over time, so he could have developed a sensitivity to the Z/D over time.
I would try home cooked or raw, or one of the limited ingredient commercial foods. The fewer ingredients and fewer additives, the easier it will be to figure out what he can tolerate. The more control you have over what he eats, the better. One thing I have found that helps Fletcher (IBD/IBS, I didn't biopsy either) with a gurgly tummy is about a tsp of Manuka honey. He gets it with each meal. Good luck! It really is a roller coaster.