Positive Babesia IFA... you don't see that every day. Congrats (sort of :p)
To answer your question, I'd be very surprised if your doctor didn't start you on atovaquone (Malarone or Mepron) plus one of zithromax, biaxin, or bactrim/septra. There's a case to be made to add Alinia too.
On top of that I'd start some over-the-counter herbals like artemisinin or artesunate, as well as something like a Beyond Balance MC-BAB-2. Could add cryptolepis too.
I'd try to hit Babesia for 6 months before doing Lyme, as Lyme-antibiotics on top of all this would be a lot. You could start a Lyme herbal protocol, like Buhner, if you felt like it.
Edit: Girlie right below me makes a great point. If your doc feels like Lyme is causing the majority of the symptoms, you could make a case to do that first.
Post Edited (Mustard Seed) : 2/16/2017 8:32:48 AM (GMT-7)