I found Buhner and Jernigan's books to be very helpful, and have followed different parts of each treatment at times. I've heard top ten treatments for lyme disease is a good point of reference as well, though I haven't read it myself. You could also do some internet research on your own - the specific protocols that come to mind besides Buhner and Jernigan are Cowden and Zhang. You could also try to find an herbalist to work with - this site might help with that:
americanherbalistsguild.com/