Obviously I would suspect that the gut is harboring an infection, there can be a number of pathogens that can inhabit the gut.
Parasite testing is very hit or miss with the miss part more prevalent. Parasites come into 3 categories, worms (nematodes), cestodes (flukes, flat worms) and protozoa which are the least understood.
Rogue bacteria can harbor in the gut as well which will trigger these symptoms. Yeast/fungal is another possibility as well as viruses. It is obvious that there is some pathogen based on your symptomology.
My suspicion is protozoa or rogue bacteria based on some of the symptoms. If it was me, I would use a bombing technique that included a number of things such as caprylic acid, fresh minced garlic, neem leaf (not neem oil),
hemp oil (Nutiva et al), golden seal leaf (not root)and black seed (nigella sativa).
This is a wide sweeping approach that could possibly kill protozoa, bacteria, yeast/fungal strains. Although it would be less effective towards nematodes/cestodes in which case you can use other things.
I would test with ParaWellness Labs ($300) which is a fine lab that can pick up nematodes/cestode activity. Dr. Kevin Cahill is in NYC and offers a one stop (testing and treatment), cost is around $500.
Disclaimer: I am not a doctor so I cannot diagnose or offer treatments, the information is educational and should be shared with your healthcare provider.