Newbie here. Strangely enough, I'm also in South America for a few months and also afflicted by this illness.
OP is right
The OP is pretty spot on with respect to the current understanding of the gut microbiome. It affects a lot more than just digestion -- from depression, to sleep, to "allergies". Fecal matter transplants are also the newest treatment available. They've been proven to work, but are not yet that common (or so I'm told).
What's worked for me
I've been coping with a) an anti-inflammatory diet (read:
http://www.breakingtheviciouscycle.info/) and b) probiotics. There are periods where I can maintain the diet and I feel great, sleep great, look great. But there are periods where I have insomnia, digestive issues, etc and feel like absolute shit. Anecdotally speaking, these seem to be when something interrupts the diet or when there's a major stress event. Supposedly if you can maintain this diet for 2-3 years, your gut will heal itself. I haven't been able to do it yet.
Causes
Regarding the topic of stress, it's a factor but not the underlying cause. I quit my job at one point and took off to get away from it all. But I couldn't leave this shit behind.
Foods/chemicals are merely the triggers, so you gotta watch what you eat. I felt way better with the food in Europe. I wasn't surprised, as the EU is much much more strict with respect to the pesticides and preservatives allowed in their food. Sadly, food safety in the US and Canada is not as good as you would believe.
I've been trying to trace back exactly what it was that got my sick like this. Accutane is supposedly a big culprit and has fucked a lot of people's lives. For me, I believe it to be antibiotics I took while in Asia many years ago.
I hope the ayahuasca treatment works out. I was recommended it, but my brief look into it led me to believe it was more effective for treating addictions and such. Dunno. But I'll be following this thread closely.