I would request a small bowel biopsy to rule out Celiac disease - as I've mentioned in one of my posts I tested negative for Celiac through blood tests several times but the small bowel biopsy turned out positive.
I too became intolerant to many foods and this was because my small intestine was becoming damaged. I couldn't tolerate milk, then eggs, then soy, then peanuts! I was getting so frustrated. Now I can tolerate some milk products (depending on amount of lactose) and am looking forward to adding back in the other foods once my intestines heal.