I had luck early on in treatment using samento as instructed by my Lyme doctor. I don't know how far I would have gotten in my recovery without antibiotics, but the samento was a good starting point for me.
There is an excellent book by Stephen Harrod Buhner, called 'Healing Lyme -- Natural Healing and Prevention of Lyme Borreliosis and Its Coinfections'. You can get it on Amazon. 200+ pages. Detailed but easy to follow.
Co-infections often need to be treated differently from Lyme, and the book covers those too.