I do agree with your assessment of acute-type infections, and early studies on HIV-1,2, provided an exceptional insight to these disease forms. Cancer and other disorders such as diabetes have shown very clearly the stages precluding the formation of pathogenic etiologies of several yeast and fungal species inhabiting the human gut.
But as for a phenomenon, where candidiasis is the primary causative factor in chronic health disorders, there are missing components to the theory. It cannot provide a full diagnostic picture without the existence of immune-dysfunction on several fundamental levels. This makes the condition rare to manifest on it's own.
Parasitic organisms on the other hand, are highly adaptable creatures, that can exist in multiple hosts, without detection beyond that which causes direct damage to the host.
I have witnessed and isolated fungal species which have had indirect clinically significant affects on the patient by remote actions within the bowel system. This was through toxin releases which can be detected through mass spectrometry.
I have seen this with algae species as well. These do not always manifest in forms detectable through microscopic observation--they must be cultivated.
In my own theory, I am talking about true stealth.
These organisms will be dismissed as human cells--undoubtedly. That is because for the most part, they are human. They seem to be hybrids of some sort. I am attempting to "tease out the wild type, but it could take months, as they must reverse evolve which takes cellular energy.
I have a hunch, they might belong to the family Entamoebidae.
I have seen 3 other possible cases, and the conditions experience by these individuals could be classified as autoimmune.