I will be honest, I only skimmed the article… But I did not see any mention of exercise. Not sure if the author will read this, but the best way I know to increase metabolism is to walk or swim. Ideally work up to something more intense like yoga or weightlifting as you start to feel better. Basically, activity work at building up an appetite and eat high fiber foods.

Also check out the fodmap diet to get your gut in order before working up to exercise.