You need to protect the kidneys and liver from die-off toxins, otherwise you will have to heal these seperately. The liver is directly related to things such as allergies, energy, digestion, etc. and is the organ most often damaged by doing the diet. If you become irritable, irrational, etc. these are liver symptoms. We recommend specific ways to detox in the following posts:
There are a variety of liver herbs that help as well such as milk thistle. Vitamin C has great detoxing properties as well.
I would do a stool test that looks at a variety of gut flora (comprehensive test) and would ask your doctor about whether the stool test looks at a bunch of things or not. They usually do in case it isn’t candida.