Yes, I know it's confusing! I was very confused when I was sick and didn't know what to do. I can only suggest... Listen to your body and if you feel that antibiotics are making you sicker, then wean off of them.
For me, I liked Dr. Jernigan's protocol because it made sense to me after I read his book. Dr. Jernigan had lyme himself, restored his own health, is a teaching doctor (holds classes constantly), goes to lots of lyme conferences, is an inventor, is constantly being interviewed, and I could go on and on.
His basic philosophy is to restore one's body and make it healthy. By doing that the body kills the lyme bacteria by itself. Sounds simple right? It is and it isn't...
I followed a simple protocol at home by taking 2 of his botanicals, rotating them, plus the detoxing, eating healthy and the most difficult thing for me was addressing the stressors in my life.
I don't know if this helps or not.. I can only tell you what worked for me. If you want you can e-mail me as I would really like to help you.
Hang in there, you sound like a fighter!
Totally healed for 8 years ~ used Dr. Jernigan's protocol from his book "Beating Lyme Disease"
Our bodies are wise as they can heal themselves with some help plus detoxing daily, eating healthy. I come back to help others for others helped me when I was sick. Pay it forward!