Hi A.,
I agree with removing all milk and milk products. Not even cookies with whey in them. No milk, cheese, yogurt, ice cream, and nothing with milk or milk products in them. My son is 23 years old and when he was about your sons age, with ear infection after ear infection (and I was breastfeeding him still), we ended up at an ENT's to evaluated for tubes; and 20 years ago that was a big deal - he suggested removing milk and milk products from my breastfeeding diet and also my son's diet (and we prayed!!) - and you know what when we went back in a month, the ears were clear and remained that way. Even as my son grew into school age, he continued to put apple juice on his milk. There were times when the mom in me just really believed that as he grew, he should drink milk so I would insist and one day as he held his nose to drink his milk, I realized that his body couldn't take it and he knew it!! So, I never pressed again. He eventually can handle small doses of milk and milk products. Sometimes when someone is allergic to something, they can handle a little bit, but when they go above what that limit is, they have an adverse reaction.
I am not suggesting to forgo tubes! I just think maybe if you take away milk and milk products in the interim, it might make your little guy a bit more comfortable. I was pretty amazed!!