You will be hitting the Borrelia with the Zithromax. It may not get completely rid of the Lyme, but it will help while you are treating the Babs.
I think starting with Mepron is fine. It's a much higher dose of atovaquone than you would be getting with the malarone, unless you take 6 Malarone per day, which I've heard of only 1 person doing. When (if) you plateau on the Mepron, Malarone can be used because it has an additional anti-protozoal in it.
Do consider combining it with herbs like Artemisinin (pulsed 3 or 4 days on/ 3 or 4 days off), Elecampane or Enula, etc.
Personally, my LLMD started me on Malarone. I'm with a new LLMD now and, after nearly 6 months off Malarone, he has just told me to start Mepron (3 weeks on/1 week off).
Bottom line, all people respond differently, so, imo it doesn't matter which one you start with because you don't know ahead of time which one will be the most beneficial.
If it's less expensive or easier to get one over the other, I'd make a case with your doctor if you feel that strongly.
Good luck!