Where do we go from here and how will we know if we need to go through this for another round, what are the symptoms that would let us know this?

You will know your full results as long as you continue on a clean diet, incorporating fermented vegetables in 3-4 months AFTER you finish, because it takes the body that long (which isn’t really very long to create a new terrain) for terra-forming and to build a new “landscape”. If you are still suffering after this, then consider cycling back around for a harder-push on the anti-microbials and see if it’s another leg up the ladder. Let’s say you get 50%-60% of the way this time and then revisit the plan 6 months later. You should get another 20-30% healing after that. Most people will be fine after the program. A few may get only partial benefit and need to go another round, usually because of a really tough pathogen, (i.e. - a protozoa or antibiotic-mutated yeast, etc).