I don't have any big ideas, other than to say, keep searching for answers. You know in your gut, and he has validated that by physical reactions, that he is very allergic to something - so do not stop the quest to find the answers. I know in the area where we live that there are some great "environmental centers" that helps identify in kids the allergens they react to in the environment. I would think food dye would be one of them. I know red dye #40 is a bigee for a lot of kids, but other than that, I am not sure. I would call around, and find a doctor that wants to dig a little deeper. There are many great ads in Child magazine for just this sort of thing.
Good luck............
