@MAF14, the glycine dosage for Dr. Klenner's protodol was 1 heaping Tbsp in milk four times per day. The other details of his protocol and info on why each item are here http://www.townsendletter.com/Klenner/KlennerProtocol_forMS.pdf . I find it interesting that coxsackievirus can trigger MS, but that same virus is common in CFS/ME. There are some updated Klenner-like protocols on the web now that active forms of vitamins are available. It sounds like the glycine breaks down to several things, one of which is ammonia which can then convert to urea which I think is an antioxidant that is really low during MS attacks. But, for CFS/ME patients, some have problems with ammonia and might not easily get enough of it converted.
Some ideas on how to lower rT3 here: http://www.stopthethyroidmadness.com/reverse-T3/
including lowering biological stress, making sure there's enough selenium, using more T3 and less T4, making sure there is enough iron and adrenal hormones, etc.
I'm guessing @Athene* that during the development of celiac disease prior to going gluten free, when the antibodies for celiac were high, that they cross-reacted with other tissues, attacking your thyroid and adrenals and possibly BBB. Then when gluten free for long enough to lower antibodies, the effects on other parts of the body didn't reverse but neither will antibodies necessarily be left high in your system.
Thanks for the glycine clarification and adding the part about ammonia. I believe I do have an ammonia issue and just ordered some L Ornithine Alpha Ketoglutarate. Per a post from @ahmo, I saw some FMN was beneficial with her ammonia issues so I opened a bottle I had laying around. I seem to be a little more clear headed but very well could be placebo... To my dismay I'm also considering going very low protein to see if that helps.
I'm familiar with the STTM protocols, I've been taking iron, selenium, and iodine for a few months now which may have something to do with it although the same protocol year(s) ago did not have the same effect. Also, I've scored pretty decently on a recent diurnal cortsiol kit BUT also start to get sleepy around 3pm every day.