Yeah a weak or damaged natural flora is what get us infected in the first place. This, along with genes, is probably why only a minority of people get infected even though many are exposed to parasites every day.
My infection too started after an amoxicillin treatment disrupted my flora. I have regretted that treatment ever since.
Btw, have you made any sensitivity tests on the usual IBS suspects such as Blastocystis?
It's almost impossible to eradicate, any data on sensitivity would be very welcome.