FWIW, those foods -- hot dogs, nuggets, probably even the ham -- would turn my DD1 into a screaming Mimi. She can't even handle the "all natural" stuff, though the standard supermarket stuff is MUCH worse. I'm pretty sure it's due to hidden MSG in the spices/seasonings/flavorings. Orange cheese always has annatto, and cheese slices usually have phosphate additives, both of which she reacts to. Even the "healthiest" store-bought candies and baked goods usually have annatto coloring and/or phosphate baking powders, so we pretty much have to stay away from everything that comes in a package, or risk yet another meltdown.
(Oddly enough, annatto, despite being a natural coloring, has been well documented to actually cause even more
problems than the infamous yellow #5, aka tartrazine. I think it's really irresponsible of "health food" manufacturers to keep adding it to foods that children eat.
In Europe, they often use beta-carotene instead; I see no reason why they can't do the same here.)
When DD1 was a baby, I kept a food diary for several weeks, and she did seem to react to certain foods in my diet, but I couldn't make head or tail of them. I mean, Romano cheese and grapes? It wasn't until a couple of years later, when I started reading about the FAILSAFE diet, that I discovered that both of those foods are exceptionally high in natural glutamates. IIRC, glutamate basically works by overexciting the neurons in the brain, which is the last thing these sensitive little ones need.
If your DS1 does have a glutamate sensitivity, the glutamine could definitely be a problem, as it can be turned into glutamate by the body. Of course, glutamate doesn't affect everyone so badly, and I've even seen it recommended as a natural antidepressant (which would fit with its effects on your younger DS). I tend to think that glutamate sensitivity might be caused by some underlying deficiency, which leads to the brain being unable to use it properly. I've researched this in the past, but can't remember if I came up with anything.
So anyway, sorry that turned into a bit of a rant about food additives
, but the upshot is that these things can act like drugs in our children's bodies. I'd personally avoid new supplements, and all processed foods, until things start to settle down. It's complicated enough already.
BTW, since he'll eat ham and sweet things, have you tried making homemade sausage with ground pork and honey? It's pretty popular here.