I don't have a similar experience but I do have some advice: if you are grain, legume and dairy intolerant, your gut flora may have been suffering quite badly. That means that some foods that are broken down mostly in your large intestine (like fruit) can't be processed, as you don't have the right bacteria (or the right amount of said bacteria) to break them down.
Spend another month eating Primally: lots of varied starches (to balance the fact you won't be having nuts or fruit), meat, shellfish, offal, green leafy veg and have your eggs raw-yolked, to ensure you get all the nutrients you need.
When you feel more comfortable, try yourself with starchier fruit, like slightly green bananas, and some less-allergenic nuts, like almonds and hazelnuts. Just small amounts, to feed the right bacteria and get it to start reproducting. You'll probably find that most fruit and many nuts are OK after a while, but, if you have a problem with legumes, be prepared to find some nuts still irritate your gut. On the other hand, you may actually find yourself less sensitized to some legumes also and be able to reintroduce them here and there. Just take it slow and introduce foods one at a time. If the discomfort of eating, say, apples goes after a week of having one a day, then keep them in. If you push your luck with black-eyed peas and give yourself awful pain that DOESN'T lessen next time you try them, keep them out.
Salmon is often fed chemicals in farms, to make them go "redder", so try some cheap Wild Pacific Salmon. It looks a bit grey for salmon, but that's just because it wasn't river-fished or fed chemicals. You probably won't have a problem with that.
You probably have the same problem with non-organic eggs: you're sensitized to some of the nasty chemical, lab-grown food that they feed the chickens and that invariably winds up in the yolk.