Use the 21 day strategy. Get your son clean of all the foods he is sensitive for, for at least 21 days. Than slowly introduce them back one by one. 1 food group ever 2 weeks or so. for meat take indeed the grassfed well checked versions as they have less nasty things in them. See which foods he reacts most violent to. This way you can find out what he can and can't eat.
Now I know PB doesn't say anything about chewing and how many times to chew, but make sure he chews his food properly. at least 5 times before swallowing. Chewing makes sure that enzymes that are needed for digestion are mized in with the food.