Bobbie, I won't just repeat what both Mac and Dovechick have commented upon, but will say that you don't seem to have read the protocol correctly: you should take docycycline every day, plus either roxithromycin every day or azithromycin once every three days. Roxy and azith are both macrolides and I think you might feel more if you correct this error.
You note two improvements along with the worsening of mobility and balance, which in the relatively short time you have been taking abx is good, especially bearing in mind how you were before you started.
I would say that in three months time, rather than stopping abx you should be considering judiciously beginning metronidazole or tinidazole, emailing David first to ask his advice. He doesn't bite: I'm married to him so I should know!