Hi Nglassman! First off let me say that I have not experienced what you are going through but I do have some random thoughts & maybe I can provide some helpful links:)
I would suggest visiting the "Ask Andreas" forum and using the search box to search within that forum for questions on digestion, raw diet, etc. That forum is not active, new questions are disabled, but there's a lot of info there. Andreas espouses Ayurvedic body typing & dietary principals. His book, "Timeless Secrets of Health & Rejuvenation" has a lot of info...
Bitters (I have used Gaia herbs "Sweetish" bitters) taken before meals stimulates bile flow. Also, 1/2 tsp grated ginger taken w/ a pinch of salt(according to Andreas) stimulates AGNI, the digestive "fire".
http://www.askshelley.com is very highly recommended. She used to have a forum here, it's still here in archive form. From what I've read she is VERY helpful & knowledgable. & she deals with candida.
Also, are you getting fermented foods in your diet now? Fermented foods, such as kimchi & sauerkraut are excellent for digestion. Different fermented foods host different microorganisms...gotta keep that biological diversity going on internally! An EXCELLENT resource for fermenting foods is Sandor Ellix Katz' "Wild Fermentation".
Lastly, I've checked out that website in your message & I'd like to invite you to check out the permaculture forum. Looks like you have a lot of good knowledge to share! :)