Well one would have thought the brain was involved in any experience of a human, no matter if "paranormal" or not. So really it doe snot get us very far does it?
Again, irrelevant. It's not a question of the brain being involved, it's a question of the brain causing it. The whole point of all paranormal explanations is that there is an external cause for the experiences. However, we actually know that the brain generates them all by itself. Exactly how and why it does this is irrelevant to knowing that it explains the claimed paranormal experiences.
Sure we understand what atonia is - just not how it works. We have some ideas, but nothing solid yet. So the even more confusing issue of why occasionally atonia might persist in to consciousness after the cessation of REM sleep - let's face it, it's still a mystery!
Yes, that's what I said. We don't know exactly how it works. This has nothing to do with it being an explanation for many paranormal experiences.
No, germ theory is quite independent of the antibiotics efficacy. The latter can be demonstrated by medical trails and statistics, even if we are unsure of the physiological aspects. Even then we can't be sure that the antibiotic action and illness ending are definitely linked - correlation is not causality, and other factors may be involved. A good medical statistician ca make an overwhelming case though.
It's not for all disease though is it? Prion disorders spring to mind immediately - cancer - etc, etc. And we might understand the principle, I think we do, but we still really should admit that we have very little evidence for any underlying model of the causality
You appear to have completely missed the point of the analogy. Understanding exactly how and why certain germs cause certain diseases has nothing to do with the fact that they are caused by germs. In fact, that germs don't explain all disease just makes the analogy more accurate, since sleep paralysis certainly doesn't explain all paranormal experiences. Just think back to when antibiotics were first invented. No-one had any idea how penicillin worked, but they certainly knew that it did work. Sleep paralysis is the same. We may not know exactly how it causes certain experiences, but we know that it does cause them.