Hey puppymon, thanks for the detailed post on your diagnosis. So if it's correct, damaged villi in your small intestine is preventing nutrients from being absorbed in your body. Because this damaged is caused by gluten that's why someone would have to go on a gluten-free diet. A full-body nutrient deficiency is probably preventing your healing.
Did he mention taking probiotics also? For my part I've been taking probiotics for years (Garden of Life). If not, might want to talk to him about in your next appointment. Don't make things more complicated right now. (Besides, you've probably gotten fed up with "natural" cures at this point.)