Yes, those kind of things can def. have an affect on the stomach. I would try to keep him stress free for a while and see if it keeps acting up. As to the milk intolerance, most people who are intolerant to cows milk can readily drink goat's milk. Raw is even better than pasterized. Although some people do not recommend it, my family and I drink raw goat milk on a daily basis. If they give cow milk at his school, just tell him not to take it, or throw it in the trash if they're forcing him to take a carton.
http://www.realmilk.com/
http://www.realmilk.com/