I spent about 20 minutes going through it, theres alot of things that indicate methyl cycle malfunction and low methyl cycle derivatives and basically cfs. I feel really good about your protocol at this point, that basically confirms you are on the right track in my mind. I will go through it further as I get time and see if I come up with anything else. Read that article by Rich Vank I posted a link to on his theory and study of cfs and glutathione deficiency/partial methylation block if you havent already, you seem like the typical person he was describing. Give it time, some people need several months. Im hoping hydroxyb12 will have a nice effect with you.
I was also thinking about your gut some today (lol) and I wonder if you didnt pick up a parasite. I know you tested positive for c diff, but alot of people carry that, we are all exposed to it regularly, most carry it without problems, and you are likely to pick up a parasite from food too. They are notoriously hard to test for. Raw garlic, wormwood (or something like paragone or humaworm), and diatomaceous earth are all good natural antiparasitics if you are interested.
Dr Conley is an awesome cfs doc btw.