I believe a restrictive low-carb phase is a good way to begin because of what you described--finally realizing what healthy feels like.

I don't believe a whole foods lifestyle causes sensitivities; I do believe it helps reveal them by reducing our overall inflammation to a point where we can notice/identify irritants. If you're in bright sunlight for an hour, you'll have trouble seeing when you first enter a dim cave--if you wait a while, you'll become more sensitive to light again and you'll start to see details.

I think just avoiding the irritants isn't the full solution, though. You need probiotics and the widest possible variety of whole foods to rebuild a healthy gut community. If you've been eating a small list of foods for a while, a slow approach to adding more will be best. Add small amounts of a fresh vegetable/fruit every day for a few days rather than a large serving all at once. That's particularly so with probiotics--I started with a tablespoon of water kefir per day for several days before trying larger servings. A few bites per day of the new food is plenty and will allow your gut to adjust. The more damage you have, the slower you'll have to go.

I don't know if probiotic capsules are a good solution; they may help but I personally use probiotic FOODS--I drink water kefir and I eat home-made yogurt and good quality store-bought sauerkraut. I also eat lots of fresh vegetables and fruits to feed my gut (and me.)

Add fruit back. A decent amount of it. And not just berries. I'd start with apples or oranges.

The fruit might make you a little gassy for a few days while you readjust to it. It will go away.

I think it's possible. Like you, I did much better without grains and dairy; then I went full-bore "paleo" and for a handful of months or so went keto (I experimented with re-introducing dairy but went for quite awhile without it, too, and felt better). However, this is when I started seeing very dark circles under my eyes and people told me I looked tired even when I was fully rested. After quite a bit of research I figured that this was correlated with food sensitivities.

I haven't fully figured this out yet by any means, and probably never will, but one of the possibilities that I've entertained is that the abundant ketones produced in a ketogenic diet, owing to volatility, are sensitizing to some of us predisposed toward reactivity (Especially, I imagine, those of us with pre-existing food sensitivities such as gluten, dairy, eggs, etc. Probably also a history of antibiotic use, fungal infections and aspartame - at least in my case). As in wikipedia's description of ketones: "ketones tend not to "self-associate" and are more volatile than alcohols and carboxylic acids of comparable molecular weights. These factors relate to pervasiveness of ketones in perfumery and as solvents" - this struck me because volatile chemicals cause strong reactions for me, such as alcohol, perfumes, etc. http://en.wikipedia.org/wiki/Ketone

Over-expression of TRP channels is likely responsible for the reactions; discovered through some research and other people's revelations on salicylate sensitivity forums. TRP channels are activated by noxious chemicals of various types. I'm not sure based on your list of foods if this is what you're experiencing, but since you noted a ketogenic diet prompting the reactions I tend to wonder. Seems like a trend.

Paradoxically though I still feel better when I'm in ketogenic mode and am trying to get back to it, albeit with a less chemically caustic diet than I once had. It's pretty boring (especially sans berries and coffee) but seems to be the only way I lose weight and feel clear-headed. Very confusing. My biochemistry background is sparse so I'm just stumbling in the dark and hoping someone out there figures this out.