As has been pointed out, there are lots of processes and interactions going on in the gut.
It is not unlikely that things that would normally be tolerated buy a healthy gut (or a healthy gut microbiome) might not be tolerated by an unhealthy gut (or disbiosis[1]).
There is a lot of debate about "proving" or "disproving" non-celiac gluten intolerance is 'just' fodmaps. I don't think it matters what it is. Eliminating wheat (gluten and FOODMAP fodmap) is a pretty basic start.
Whether wheat is something that is making you sick, or something that you could tolerate if you weren't sick doesn't matter.
Unfortunately, 'giving things up and seeing if you feel better' one at a time is not adequate to know for sure.
You might be lucky, you might hit the big problem straight away, like an undiagnosed celiac saying "hey, i think i'll try gluten free".
But if you are ill you might not able to digest, might not be able to heal, so might not feel much better. Your microbiome could be so heavily disrupted and your intestine so heavily ulcerated, that it just isn't enough.
If i was feeling pretty healthy i might play about to see if giving some things up was all i had to do, maybe add in a few missing ingredients (vitamins, fibre, good fats, probiotics).
If i was feeling that i had to hurry, or would rather be thorough and get it over with only once then i would research
ALL the foods that
MIGHT be a problem (certain proteins, fodmaps,chemicals,processed foods, anything that contains 'natural flavours',sugar,etc,etc)
For a short while one would eat only from a limited selection of foods and eliminate everything else.
Then, at appropriate intervals, reintroduce one food at a time to see if it is tolerated.
What food you reintroduced depending on your appetite, and but mainly keeping in mind how risky that food could be.
I thing anyone with digestive issues should think about what food really is and why.
Well cooked, easily digestible meat and vegetables are reintroduced first to create a bit of variety and maximise nutrition, starting with broths, moving to soups, and then solids.
The foods that might be a problem, things like nuts, eggs, tomatoes, or dairy are last, and some like gluten or sugar are never used again by many.
I would recommend looking at ....
(only a suggestion)
The Paleo A/I (Auto-immune) Protocol, - google "the paleo mum"
(not that i think crohns is an autoimmne disease - only that it is a well thought out (from a paleo perspective) attempt to eat well and correct disbiosis in order to heal.)
I would look at others diets like fodmaps, and SCD and work out what you want to do to see if you feel better
[1] Disbiosis - Wikipedia
https://en.wikipedia.org/wiki/Dysbiosis
Clinical consequences of diet-induced dysbiosis
"We introduce the complex tripartite relationship between diet, microbes and the gut epithelium. This is followed by a summary of clinical evidence of diet-induced dysbiosis as a contributing factor in the development of gastrointestinal diseases like inflammatory bowel disease"
https://www.ncbi.nlm.nih.gov/pubmed/24217034
would love to see the whole article......