My guess is that CFS is a mixture of autoimmune dysfunction like you said, neurotransmitter disorders, and one or more other things, depending on the person/specifics..
One of the worst concepts ever advanced was presented to me when I was in training (some time in mid 1700's!) was that the brain is an "immune privileged site". Utter hogwash as it turned out and it has set back the understanding of depression, Alzheimer's disease, and a bunch of other refractory problems very significantly a for quite a long time. The CNS has its own dedicated immune system in terms of glial and astrocyte populations with glial cells as the resident phagocytes. And this local system of course is in constant communication with the immune system in the periphery.
Anything that affects the immune system affects neuroplasticity, circadian regulation, and multiple amine and neuropeptide systems in ways that we barely can index or measure. The immune system is inter penetrant with every other signaling system in the CNS and with behavior directly in ways even most physicians don't often full appreciate. We know this because of the conserved syndrome of "sickness Behavior" which is shown in all vertebrates and which reflects the inhibiting effect that pro inflammatory cytokines have on the deep motivational systems in the midbrain, somewhat mis-categorized as "the reward system". It's more a system for the seeking of rewards in other words for generalized motivational arousal and it has a bunch of other connections to other brainstem and subcortical systems. But it's pretty clear that sickness behavior is a conserved part of immunocompetence such that we go home and rest or perhaps more colloquially we slink back to our cave and sleep it off. This actually improves our immunocompetence. If on the other hand we resist this ancient program, try to run around in the world and do our normal activities when we are seriously ill we find we are saddled with fatigue, cognitive fog, and anything but our best performance, and the performance of our immune system suffers too. In this sense organism defense against pathogens and running around in the world/learning and neuroplasticity ("doing our thing") are functionally counterposed vectors. You can't optimize for both.
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