I'm so sorry your toddler is having problems! From what you describe, it does sound like the culprit could be wheat allergy or gluten intolerance/Celiac. Which tests did you have run? Skin prick test for wheat allergy and blood test for Celiac? The most conclusive test for Celiac would be an intestinal biopsy, but if your child has been off of gluten, the damage may heal to the point that the test is falsely negative. For wheat allergy, I would skin test and blood test to try and get an "on paper" diagnosis, but neither test is definitive and reaction history always trumps testing.
I'm hoping members with Celiac, wheat allergy and, since it sounds like you may be in the UK, UK members will join in the conversation and be able to give you better suggestions and resources than I am able to.