Sorry to hear about all the things you are going through...I don't have mitrochondrial disease, but I do have leaky gut and it has been hell with IBS, constipation and gut bacteria and fungus, along with all the food allergies I am experiencing. My MD, a doctor of osteopathy, who believes in alternative medicine, suggested me taking North Amercian Herb and Spice Inflam-eez (10 of these a day) for the gut inflammation and also Living Clay Detox Clay Powder (4 teaspoons a day mixed in 4 oz water (I also put in 2 tablespoons of organic apple cider vinegar to help the clay mix well)). Both of these have helped me alot in healing the gut issues. You didn't say whether you have gut bacteria and fungus (traditional doctors are so inept diagnosing these). The MD also has me take daily probiotics.
IMPORTANT: IMPORTANT: When you first start taking the clay, start with 1/2 teaspoon, see how you react (the clay causes detox symptoms, as it is cleaning out your colon - achy body, flu-like symptoms, sore throat, etc). If you feel OK, then continue to up the dosage a half a teaspoon until you are up to 4 teaspoons a day. Every time you up the dosage, see how you feel and adjust upward or downward accordingly until you are at the full dosage.
I hope this helps...it sure helped me!