Have you pursued the possibility of an autistm/ADHD diagnosis at all? In my experience (as an autistic person with autistic children and siblings) the signs of autism can be uneven, despite it being a lifelong condition, because the experience of being autistic can be aggravated by environmental conditions and stressors, developmental stages (especially puberty) and by the uneven demands placed on kids by the stepwise development expected at school.
Looking at the list of symptoms on the PANDAS page, I was struck, for instance, by things like 'sudden deterioration in visuospatial skills' and 'clumsiness'. That might well relate to the dyspraxia that autistic kids often also have, but might only become apparent when they're suddenly expected to change into PE kit independently when they haven't before - the onset isn't actually sudden, just the visibility of the problem. I get that you feel it followed a physical illness, but autistic children (and adults for that matter) often somatise, i.e. complain of feeling ill when actually they're (we're!) dysregulated. If other stressors ease off, then the feeling of malaise eases off too.
These are just examples, but the point I'm making is that the idea of the autistic experience being a consistent one, in contrast with this syndrome of your DD's, isn't entirely accurate or helpful. I often feel that I'm "particularly autistic at the moment" when external demands mean that, say, sensory things that I could normally cope with become intolerable.
I can't help feeling that this PANS/PANDAS thing might have been dreamt up based on the observations of parents who have no idea their child is autistic. When I think how hard it was to get an autism diagnosis, there's no question in my mind that going to the doctor with a loose collection of traits plus a complaint of feeling unwell would probably not have led to the correct diagnosis and might instead have led to a wild goose chase after a mystery illness. It's not surprising that parents without the family history to make ASD/ADHD an obvious starting point might end up thinking their child has some new and complicated syndrome. If you can bear to, I wonder if going back to conventional medicine might offer you more answers than you think.
Apologies if this is patronising. I just remember being gobsmacked by how many seemingly mysterious aspects of my own health and daily experience were fully explained once I re-examined them through the prism of an autism diagnosis I hadn't previously considered. I'm happy to discuss mine and my children's experiences by PM, if that would be helpful.