I think you can drive yourself mad trying to figure out the etiology. I have tried to do this myself too. Maybe a less stressful approach might be to figure out as much as you can about what is wrong and address each one.
If it were me, I would start with strict diet to reduce fermenation as much as possible (which you have done), then do the methylation panel and address that if neceseary. If the glutahtione is reasonable I would then start chelation and when that is going I would start to test for various viruses and bacteria.
And when you're strong enough, do measures to address that gut - I fast 1 week out of 8 and do a biofilm protocal every other week.