I'd say you are on the right track in concentrating on getting the gut sorted out. Without proper absorption and digestion, we can't hope to get well.
Have you been down the path of going to a very simple diet and then adding things back in one at a time?
So for instance avoid all dairy.
Avoid all grains.
Avoid all soy.
Avoid all manufactured and highly processed 'foods.'
Avoid soft drinks.
Avoid eggs.
What about allergy tests?