So are you looking for the grand unifying theory of health and wellness? Whatever it is, it does not have to say that bacteria, viruses, protozoa, etc don't cause disease. (The great majority of them do not, that is correct, but many do.) Newtons laws still hold up after 19th and 20th century advancements in scientific knowledge. Much of what you've posted is about what we can be doing better. Doctors over-prescribe antibiotics. No shit. That doesn't mean that the idea of healing a person with a parasitic bacterial infection with an antibiotic (when we know exactly what the chemical does to halt the growth of its target organism) goes out the window.
Hopefully we will move beyond traditional antimicrobials. I tend to think the ongoing struggle with these types of disease will not end in our lifetimes. I just have to say that the "Germ Theory is wrong" statement really grinds my gears. I'll accept "the Germ Theory leaves much to be desired in terms of explaining everything that goes wrong with us."