If there's a history of antibiotics and at any time he had a yeast overgrowth in the gut, leaky gut may well be part of the food problem as well. For Josie we had to cut out ALL sugar, including fruit, juice, agave, even dairy (which you're cutting out anyway), and most grains, to kill the yeast in her system; we stuck with that diet for about 2 months before adding things back in. I'm fairly sure that by now it's a problem again, but as long as we keep the diet strictly under control, we see FAR fewer problems behaviorally and digestively than we ever used to.
Leaky gut would come from the yeast overgrowth and would actually allow undigested protein molecules, like casein and gluten, to pass right into the bloodstream, triggering allergic reactions to them. And the yeast, when they're fed, produce carbon dioxide, resulting in nasty gas and diarrhea, often within a short time after the food is eaten, plus the other chemicals yeast produce can mess with blood chemistry, which in turn messes with brain chemistry and can cause behavior things.
The program we followed was the Body Ecology Diet, and while it's REALLY REALLY strict, I also found that I lost 30 pounds of stubborn baby fat while we ate that way AND nobody in the house got even remotely sick for three months in the Winter, even with a kid in preschool (aka "germ factory"). Googling "Body Ecology Diet" should give you some info about it, or you can just go to
http://www.bodyecologydiet.com for more info.
You can also ask about Grapefruit Seed Extract, which I've even seen advised for nursing moms with thrush; it kills the systemic yeast in the system. I make Josie "juice" drinks by putting either some lemon juice or plain unsweetened cranberry juice in the bottom of a bottle or pitcher, adding some GSE, sweetening with stevia (herbal sweetener, does not feed yeast), and topping off with water to make "lemonade" (or "cranberry-ade" LOL). She'll drink a good half-gallon of that a day if I let her, although I do encourage water more often, maybe alternate a juice drink with a water drink.
Anyway, I didn't know if any of that might raise a red flag or ring a bell for you, so wanted to put that out there as another possibility.