I do agree with Michelle that food can often be a problem for people with autoimmune diseases. Research hypoallergenic diets and at least try a diet free of major allergens (gluten, dairy, eggs, shellfish, possibly soy). Get plenty of probitics (not cow's milk but coconut, soy, or goat's milk) or in supplement form. Get plenty of enzymes, which would help to eat raw like Michelle recommends, or even take some plant-based enzyme supplements when you eat, but don't depend on them forever, or your body will may less of its own eventually. Fresh pineapple is a good source of enzymes and is often recommended for those with RA (another autoimmune disease) in getting rid of immune complexes in the body and reducing the autoimmune response.
Research different amino acids and melatonin for sleep/mood issues. Also research low dose naltrexone and alpha lipoic acid treatment to see what you think.