Autonomic dysfunction in itself is enough to make you feel totally miserable (I know because I have it), but I'd advise a bit of caution in that, as far as I know, it's rarely the primary condition (there's usually a secondary cause - often ME) and treating it will only really be addressing the symptoms (plus there aren't a whole lot of specific treatments).
A good clue to dysautonomia is that your basic bloodwork is fine (WBC, ESR, CRP) but your vitals (BP, HR) are all over the place and you feel like you're running a temperature / have the flu even though your temp is normal or sometimes even mildly hypothermic.
Perhaps the next time your daughter is feeling at her worst check all of the above (BP, heart rate and body temperature) just to get an indication of what's going on. When I do this, I find that I'm mildly hypotensive (I'm usually on the other side of it), and my body temperature is about 35C -- which is mildly hypothermic.
After a few hours, when the worst of it has worn off, my vitals are back to normal.