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Sounds very frustrating. Have you tried getting on some good liver herbs and staying on them a while? All around I would consider digestion. You don’t seem to be benefitting for your food for some reason. I think dysbiosis is more of a symptom than a cause. If things higher up like the pancreas and liver, stomach acid.. Are working right bacteria should be right.
Also, have you tracked your food intake? I know you say you’ve stuffed yourself but I e seen lots of people who thought they were eating a lot until they tracked and they found they were undereating. You want to eat about 500 calories over your current TDEE to gain. http://www.health-calc.com/diet/energy-expenditure-advanced
And hate to say it but, there could always be something genetic you simply cannot fix and can only manage.