I wish I had some good news for you, but I don't.
Bartonella is really difficult to eliminate. I found it to be resistant to many antibiotics, including rifampin, clarithromycin, amoxicillin, and cefdinir.
Doxycycline is one of the few drugs that bartonella has not been reported to be resistant to, but as you're probably figured out, that may not be enough to eliminate it.
I've described what I ended up taking here
https://www.healingwell.com/community/default.aspx?f=30&m=4136852While I did find some antibiotics that would work against bartonella, I had to take some 'strong' stuff that had unpleasant side effects, and I'm still not sure the infection is completely gone.