golden , stimulating the brain to adapt is about stimulating the parts you want to change, and in the direction you want to change. That is what CBT is about too. Visualizing what you want to do, visualize yourself doing it, as a daily routine and you are on your way. With something physical then doing it is important, even if most of that is mental. However such visualization can still cause PEM I think, though not as badly nor as easily as actually doing stuff. Physiotherapy in stroke or other brain injury patients can help retrain the brain.
My best guess is that the brain is damaged as a secondary consequence to immune issues, but that such damage is typically neither severe nor irreversible. However the immune problems have to be fixed first before the brain can fully heal, and we don't know how to do that. My leading cause for the problem is enteroviruses, given that recent advancements in our knowledge of them change the whole picture of what such a virus can do. I do think that methylation problems, and EDS, and any oxidative stress inducing disorder exacerbates this, and also increases the risk of getting this problem.
When I say the brain damage is not severe, I mean that most of the problem is metabolic, hormonal or immune, and the underlying brain structure is mostly intact.
Physical injury to the brain stem/upper spine can sometimes be alleviated and Wayne is right that if this is a problem for a patient then dealing with it can help. However I had many long talks with a chiari patient who had surgery once, and this is a path you want to be careful with as its also possible to further damage the brain stem/upper spinal chord.
