I am not a doctor and can not say, but have you considered that all of these issues may be the result of a parasite infestation?
If your body is reacting to microbes that should normally be predominant in your intestines, then something is causing that problem. This is especially true if you react to most normal natural forms of probiotics.
Have you tried Kimche? Sauer Kraut? How about Natto or other fermented bean products?