Good to hear about your experience so far!
If you haven't seen this incredible video about MS and a primal diet, check it out, Dr. Whals who has MS herself. But it sounds like you already understant the whole mitochondria thing.
The Autoimmune Protocol can be found at Robb Wolf's site, but I'll put it for you here:
Paleo For Autoimmunity
Emerging research has made clear the link between Neolithic foods (grains, legumes and dairy) and autoimmune diseases such as Lupus, Rheumatoid Arthritis, Multiple Sclerosis and a host of other less well know conditions. Many people have found significant improvements in autoimmune disease by eliminating the Neolithic foods and building a diet around nutritious Paleo options. If you suffer from an autoimmune disease we highly recommend you start a Paleo diet and let us know what your results are. To give your body its best chance to heal we recommend that you initially limit the following foods:
Tomatoes & eggplants
Peppers including bell peppers and hot peppers
Spices such as curries, paprika, and chili powder.
Some of these otherwise Paleo-friendly foods have been shown to be problematic in individuals with autoimmune issues. We recommend you fully remove not only these foods but also all Neolithic foods (grains, breads, potatoes, beans and dairy) for at least a month to see if they pose a problem for you.
Good luck with your health and I look forward to updates!