I'm no expert at all, but I would try a GAPS type diet with lots of bone broth, fermented foods, avoidance of any sugars outside of tubers. Stick with meats, good fats, cooked leafy greens, sweet potatoes. Also as much rest as you can manage. Give that several weeks, then gradually add in foods to see how they affect you.
It sounds like your body has had a rough time with chronic infections and long term medical issues. You may need a period of deep healing to break the cycle of your body hyperreacting to any irritants.