Perhaps he is lactose intolerant? My son was, back when he was still on milk. If someone is lactose intolerant, then the gut isn’t able to fully break down the lactose in dairy products. The symptoms of this are usually gas and discomfort. If Lactaid doesn’t make a difference, then at least you know it’s NOT a lactose issue, and perhaps you would need to try a milk substitute (like soy, hemp, rice, potato, or goat’s milk).
You could try treating the whole milk with Lactaid drops to see if that resolves the gas and night waking. There are lactose-free milks available, but I was never able to find a full fat/whole milk one – usually just 1 or 2%. With the lactaid drops, you add between 5 and 15 drops per liter and it works best if added 24 hours before drinking. When my son was on milk, I would typically add about 34 drops of Lactaid to a fresh 4 litre jug of milk just as he was getting to the bottom of the last jug. That way it had about 24 hours or so to break down the lactose before he started to drink it. As soon as we started doing this, his gas issues stopped.
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