I'm sorry you feel like this, but this forum has helped me tremendously... I've noticed that your previous posts were not unanswered.
What you describe as a flare seems a herx to me, especially because it happened after she started abx; And her symptoms say Bartonella, in my personal opinion.
It is very difficult to distinguish herxes from flares and symptoms - only after almost a year of treatment I suddenly saw the light - lol. Now I'm pretty confident about distinguishing flares from herxes.
I would advice you to go through the 'New to Lyme?.... Start here!' thread on top of the Lyme page, you can find lots of information about detoxing there. You can help your daughter with doing the dry skin brushing, and giving her epsom salt/peroxide baths, giving her plenty of water to drink (with lemon, if she isn't suffering from muscle twitching or muscle spasms).
My dr didn't say anything about diets either, but he had put me on a sugar free diet before, and other eliminating diets, maybe he considered that enough. But I would advice you to go off sugar, try to eat gluten free and if possible dairy free. Gluten and dairy increase inflammation, not a good thing while being treated for Lyme and co.
I received Azythromycin for Bart, combined with Plaquenil and Minocycline, then Rifampicin with Tetralysal, then Azythromycin with Tetralysal.
A good dr sould be able to diagnose based upon clinical manifestations of Lyme, cause the existing tests are highly inaccurate. I myself only tested positive on the 41 band, but then positive on an Elispot LTT test, and I have an almost complete Lyme and Bart symptom list.
I don't know about band 41 and virusses????
I think your dr knows what she's doing...