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I would get all the hormones checked first and a general blood screen, just to see how everything is doing internally. If it is an autoimmune disease, I would imagine that the white blood cell count would be pretty high...
But since you say he came home fine and then started to break out, have you looked at maybe household products? (Like fabric softeners, detergents, cleaners, etc) Could be that he is allergic to one of those, in addition to a food allergy.
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