Sorry to hear you are feeling so bad.
I am also on Mepron and it took about 3 months to feel better. Mepron has some very real side effects that can seem like a herx. The side effects are pretty common too. They seemed to dissipate slowly over time. Babesia itself is at least as bad as lyme! Even worse it makes the lyme harder to treat. I just read a scientific report that found a substance in the parasite actually turns off one of our own defense mechanisms that fights the lyme bacteria. I think this may why some doctors want to treat coinfections first. (although bartonella doesn't have this characteristic).
I feel like I have made significant progress in reducing a lot of my symptoms, so try to hang in there! I hope you start to have some good days too!!
I will keep you in my thoughts,
Anna