Julia,
    I had numerous problems from foods for years.  Eliminating milk helped
greatly, but like your son, I continued to have problems.  It turned out that
the basis of my problems was actually the gluten causing inflammation and
sensitivities in the body.  Once irritated the body then is sensitive to ANY foods
which have similar molecular structure such as casein and soy.
    Check out the site:   www.enterolab.com
    I tested there showing that I had gluten sensitivity as well as casein,
yeast and egg problems.
    I'm 90 % better now as long as I stay on a strict casein free gluten free
diet.  Then occasionally rotate in the other foods which might also cause
sensitivities such as soy, egg,  or yeast.
JL