Terrain vs. Flora

There's a book by John Thomas called "Young Again", where he discourses on pH and terrain management. It makes a lot of sense, and he goes into Liver Flushing and colonics a great deal. So it could be a matter of putting the cart before the horse:

a) do bacteria/fungi/virii alter or influence the terrain, or
b) does the terrain influence gut flora?

... and once the gut flora is thrown off, and the anaerobic organisms begin to dominate, this leads to its own subset of problems, [systemic] Candidiasis included? John Thomas and certain others like Dr. Young believe b); this opens up a huge can of worms because if b) is true, it means important tenets of medical Science will have to be rewritten.

I've also read Candida Albicans' purpose is to 'morph' into its fungal form and then rot the body from the inside out, when its host dies. Until the body expires, it exists as a benign yeast present in pretty much all bodies, both healthy and ill. If true, the question becomes 'what is the signal that causes candida to turn fungal and destroy the body'? Finding and correcting this would theoretically solve the problem.

Some hypothesize many people (esp. in industrialized countries) have issues with not being able to absorb their food, thus the hotly-debated point of whether or not people have putrefactive buildup of some sort (old rotted food, or mucous) in their colon. If so, this would explain why some people change their whole diets (the Atkins-esque diets nowadays, or Candida diet protocol) and fail to achieve any notable success. At that point, it wouldn't matter what quality food e.g. green veggies and the like one would consume; it goes in one end and out the other, with the body not really being able to enjoy its food. So what starts this process in motion? A congested liver? Gut inflammation (or as Edgar Cayce mentioned in a lot of his readings, "irritations")?

Moreover, how could one fully recover? Would easily-absorbable green drinks (ala Dr. Young) do the trick? Or would the LGS/Candida/CRS condition overcome that too? Colon cleansing? Liver flushing? I've done the latter two for awhile now and they have helped somewhat but I'm not where I need to be healthwise- yet. JV, you have an excellent point on the question of why some people use Antibiotics and recover quickly whilst for some it ends up being the first step on a road to ill health.