My nieces ate very well. In each instance, they had interesting and tasty foods to enjoy. In at least one instance (Tony's), their food was far better than what we ate from the menu!
As for breakfasts, I believe they had bread and hashbrowns...eggs....a beautiful fruit assortment...pancakes...
That's what I remember for now. If wheat is a problem, most of the kitchens already have a wheat substitute flour on hand...but even if the substitute is no good, they are very good at accommodating dietary needs.
This is truly a place where WDW shines above most vacation destinations! The chefs truly give individualized attention to those with food allergies.
I have confidence your son will feel special and his meals will add to the magic of your vacation!