Just my opinion here - I think that one aspect that is sometimes overlooked in the molecular mimicry theory is the role of gut permeability.
Totally agree with you on that one!
I think of disease activity as being described by a multi-dimensional equation[1], so the only way to characterize the effects of a single variable is to hold everything else constant. Sadly, that's impossible in real life. Since factors other than microbial population are changing, then you could easily get random-seeming changes even while consistently "starving the bad bugs".
One of the other main factors must be gut permeability, which explains why so many people with severe AS also have serious digestive symptoms. Managing to heal gut problems seems to be a consistent theme among the diet success stories. Conversely, eating things that bacteria don't care for but your body doesn't like either is not too helpful... for instance nut and dairy allergies could sabotage some people's attempts at LSD/NSD.
There are also other things that can stir up the immune system, including injuries or other illness, so that the response to ever-present triggers such as Klebsiella (or something similar) gets amplified. For instance, my immune system went into a state of high alert as an after-effect of a low-speed car accident, and I went into a flare without any diet changes or digestive upsets. I suspect flares can be caused by fighting off viruses, even ones that are "sub-clinical" so you don't really notice being sick (just being flared for no apparent reason).
[1] Math is fun! Really! But it helps to have had a good teacher.
