I agree with Mr Mike. If you really want to understand these infections you should read his books.
The "Healing Lyme" book and original "Herbal Antibiotics" are outdated, although they still contain good information. His protocols have changed since they were published, and the changes are reflected in the newer editions. Every single one of them is a wonderful resource and can be found in both hard copy and digital versions.
Herbal Antivirals: Natural Remedies for Emerging & Resistant Viral Infections
Healing Lyme Disease Coinfections: Complementary and Holistic Treatments for Bartonella and Mycoplasma
Natural Treatments for Lyme Coinfections: Anaplasma, Babesia, and Ehrlichia
Herbal Antibiotics, 2nd Edition: Natural Alternatives for Treating Drug-resistant Bacteria
According to Buhner's facebook page, the new lyme, chlamydia and rickettsia coinfection book should be out in November of this year.
/www.facebook.com/stephen.buhnerBuhner no longer updates his website, so the information you find there will also be dated. For more current info, go to the facebook page, although he doesn't answer too many questions there.
A WORD OF WARNING:
The dosages posted on Buhner's website and in his books are only suggestions of maximum dosages. DO NOT START AT THESE DOSAGES.
Start with single drops of tinctures or very small amounts of dried herbs and gradually (over the course of weeks), increase to the point of herxing. Do not increase dosages further if you are herxing. Do not add other herbs if you are herxing. Either stay at that dosage or back down a little for a couple of weeks. Die-off will continue, but at a pace that your body is capable of detoxing.
Add only one herb at a time so you can observe your reaction to it.
As for figuring out where to start, I would start with the protocol that explains your symptoms to the greatest degree, and once that it up and going, start adding herbs from other protocols.
If your symptoms are babs, I would treat that first. The mycoplasma protocol is very nutritionally based and you can address diet right away, so do that as well.
It sounds like you need to read both the bartonella and babesia books. You won't be disappointed. Just be ready for a paradigm shift in the way you think about
infective organisms.