Candida wrong target?

Hi shroom...I wouldn't disagree with your hypothesis. In fact I would extend it because when you have serious candida issues,  it is now fairly well known that this disease is highly associative with other diseases caused by bacteria, parasites, viruses, mycoplasma etc. So when your candida gets serious,  your immune system bar is lowered tremendously which eventually allows in all manner of different pathogen species into the body. 

Here is some of the evidence and research on these candida pathogen association from Dr Wiliam Shaw:

Candida and Yeast Overgrowth

Furthermore, you mention only amoeba inhabiting the intestines. It is also well known through research that candida is a dimorphic organism -- it has two distinct and differing living forms. It has a yeast form -- a saprophytic feeder, reproduces by budding -- and it also has a fungal form -- a true parasite, reproduces by spores. 

The yeast form inhabits locally -- uterus, skin, intestines etc. The fungal form infects the blood, organs and tissues -- everywhere in the body in other words. 

What I'm trying to say is that if you don't make specific effort to get rid of the systemic candida from both the intestines(yeast form) and the blood(fungal form) then you will probably never get rid of it or it will just keep coming back. 

Eight years ago I used a multi-protocol to sucessfully cure my own serious candida issues. This protocol has also proved quite successful for other people who have candida. This protocol was particularly aimed at removing both the yeast and fungal forms of candida. Here are just the pathogen-kill protocols that I used, defined in detail:

Anti-candida Protocols 

I must also emphasize that the above protocols were only a part of my own muti-protocol regimen. The other parts of my protocol consist of more detoxing, supporting the liver/kidneys and a simple diet.