1.) MS and RA are “aged” diseases not overactive ones per the below 2005 National Institute of Health(NIH), 2004 National Institute of Arthritis Health(NIAH) & 2000 Mayo studies.
A. http://www.ncbi.nlm.nih.gov/pubmed/16126966?dopt=Abstract
B. http://www.niams.nih.gov/News_and_Events/Spotlight_on_Research/2004/ra_marker.asp
C. Mayo link is no longer available but I had copied it into a text file if you want to review it.

 2.) Some patients with MS experience what they call “Brain Fog.” An example of this is a person was on their way to thei sister's house and half way there forgot where she was going and did not know where she was at. However, long term memory does not seem to be affected as much. Sounds like a form of dementia or Alzheimer's a disease found in our aged population. The below article is entitled 'Ties Vitamin B12 and Foliate Deficiencies With Alzheimer's Disease.” Another symptom that may very well have something to do with vitamin deficiency. http://www.sciencedaily.com/releases/2001/05/010508083559.htm

3.) Per the International Journal of MS Care, less than half of the studies participants with MS had normal bone density. Thus, they have a disease that is in part due to not enough vitamins mostly seen in aged populations.
http://www.osteopenia3.com/Osteopenia-MS.html

4.) Multiple studies, including government studies, show that low vitamin D puts you at a greater risk for MS.  So adding vitamins reduces risk of Multiple Sclerosis (MS). So again, is it that great a leap to think the disease process is due in part to vitamin deficiency in most cases due to malabsorption?

MS
http://www.ncbi.nlm.nih.gov/pubmed/11115787
http://www.ncbi.nlm.nih.gov/pubmed/9316607
http://www.ncbi.nlm.nih.gov/pubmed/18655192
http://www.ncbi.nlm.nih.gov/pubmed/17823429 -D3 safe at higher doses info.

BTW Vitamin D is activated by certain UV rays on the skin (ONLY in summer). The liver then processes it into 25, hydroxyvitamin D. At this point it is used throughout the cells of your body. If calcium is low in the body, the kidneys process it down further into 1,25 hydroxyvitamin D which triggers your bowels to absorb more calcium. So low D can cause low calcium. The FDA in Nov 2008 has now doubled the requirements for D in children. Since other NIH studies have shown this vitamin can reduce the risk of autoimmune disease like MS, diabetes, osteoporosis, heart disease and certain types of cancer. If you are interested check to see if your multivitamin has at least 1500 IU of D3(more potent) and take it with fishoil, nuts or food with olive oil.  The reason is vitamin D (A,E & K) is fat soluable. So it has to have fat in gut for it to be absorbed well. If you want, ask your doctor for more information.

RA
http://www.ncbi.nlm.nih.gov/pubmed/18594491
http://www.ncbi.nlm.nih.gov/pubmed/18682414

 FYI Resistin is produced by liver and if it is too high is also an indication insulin reistance may be occuring. If your liver is healthy this number will be lower while adiponectin(good) is higher. These two liver tests might be good to ask your doctor for since they are not commonly looked at yet.

5.) Estriol(good estrogen) seems to be helping some women with MS but not others. They do not know why some are helped and others are not?? After looking into this further I found that B12 is needed for DNA and myelin sheath synthesis. Per the University of Utah Physiology department, estriol is a requirement for certain vitamin absorption ie Vit D, Calcium, B12, folic acid(B9) and other B vitamins. Estriol aids absorption because it is required by the liver to produce transporter proteins. These proteins, as their name suggests, transports vitamins into the body so your cells can use them. Thus, if your absorption problem lies in low levels of estriol(due to adrenal fatigue, etc) then adding estriol will help you absorb nutrients and give your cells what they need to repair themselves. However, if your problem is low intrinsic factors in your stomach then low estriol is not your problem and taking more estriol will not help you. This seems like a very logical reason to me why it helps some and not others. This information also shows how the endocrine system plays a role in absorption and immune function.
(See my B12 flowchart to see how liver needs estriol to make transporter proteins to bring vital nutrients into the body.)
http://www.universityofcalifornia.edu/news/article/8978
http://www.medscape.com/viewarticle/441856
http://www.neurologyreviews.com/nov02/nr_nov02_estriol.html

6.) Everyone says stress makes their symptoms come out. What does stress do?
The effects are two fold, from what I read. It reduces absorption which also makes you more susceptable to infection that is harder to repair without enough nutrients. PLUS it leads to series of events that destroy parts of the body.
a.) It lowers absorption via many ways. How does it do this? It increases Cortisol production which lowers calcium absorption, needed for B12. It also lowers your blood pH making it more acidic. Exactly what your good gut bacteria hate ie reduces pro/prebiotics and subsequent absorption. So the bacteria die off and you get less absorption of nutrients. A more acidic blood pH increases your susceptibility to disease and infection that once they are in your system cause more damage that you are unable to repair yourself from. Stress aslo triggers more fat to be stored in areas like the omentum near the liver. Research is showing how Non-Alcoholic Fatty Liver Disease is negatively affecting the body by reducing absorption(less transporter proteins), etc.  I do have data on how body is affected by stress but how stress is then affecting the MS is my hypothesis.
http://endo.endojournals.org/cgi/content/abstract/104/2/547
http://www.ppnf.org/catalog/ppnf/Articles/Acid_alk_bal.htm

b.) Rheumatoid Arthritis: Stress leads to damage in joints http://www.niams.nih.gov/Health_Info/Osteoarthritis/default.asp
Joints are made of:

• Collagen (fiberous proteins) 
• Proteoglycans(protein+sugar+proteoglycans) These   two weave together.
• Chondrocytes (produce cartilage & release enzymes that DESTROY collagen)
  Me-So you NEED your chondrocytes but don't want them to overproduce the enzymes that DESTROY collagen.
  
  So you need proper nutrition to keep up joint health ie Vit C, Calcium, Phosphorous and Magnesium. You need to take these at least 2 hours from the time you take iron, folic acid and Vit C. This is because iron will bind to calcium and you'll just flush them down the toilet.  Always see a physician in regards to what vitamins and dosages might be right for you.
  
  
  What causes the Chondrocytes to DESTROY collagen with the enzymes it produces?
  http://cat.inist.fr/?aModele=afficheN&cpsidt=1497362

  Conclusion: breakdown of cartilage matrix by chemokines. Activated with PROinflammatory cytokines.
   Me-So Cytokines are part of the cycle increasing damage to the body.

http://findarticles.com/p/articles/mi_m0ISW/is_2003_May/ai_100767858
Skin health, eczema, and preventative strategies-Townsend Letter for Doctors and Patients,  May 2003  by Chris D. Meletis & Jason Barker

"Indigenous gastrointestinal microbes have a significant effect on the gut-associated immune system and play a large role in the development and maintenance balance between tolerance to innocuous antigens and capability of mounting an inflammatory response towards potential pathogens. Distinctive alterations in the composition of gut microbes appear to precede the manifestation of atopic disease, which suggests a role for the interaction between the intestinal immune system and specific strains of the microbes in the pathogenesis of allergic disorders. (12) Restoration of intestinal permeability, unbalanced gut microecology, improved immunological gut barrier function, and down-regulation of intestinal inflammatory responses with reduced pro-inflammatory cytokine production"
Me- So certain Probiotics, good gut bacteria, reduce pro-inflammatory cytokines. This, per the study above this one, reduces their damaging effects to body ie breakdown of cartilage matrix.

http://www.ingentaconnect.com/content/els/10107940/1999/00000015/00000003/art00038
The heart produces but the lungs consume PROinflammatory Cytokines following CardioPulmonary Bypass.

http://www.ajcn.org/cgi/content/abstract/85/2/385
Alpha Linolenic Acid Inhibits PROinflammatory cytokine production

c.) Multiple Sclerosis: How stress damages the body
http://jnnp.bmj.com/cgi/content/abstract/jnnp.2007.135681v2
Hyperalgesia (excessive sensitivity to pain) correlated with elevated proinflammatory cytokines

http://www.med.wayne.edu/Neurology/basic_research/labs.asp
Scroll down to Neuroimmunology
Studying the role of CNS endothelial cells and pericytes in Encephlomyelitis(brain & spinal cord inflammation).

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2193155
Human Growth Factor (produced by Pituitary gland) protects against Encephalomyelitis(brain & spinal cord inflammation) by switching balance of T helper cell Type 1 & 2 Cytokines within CNS.
Me - So it increases the immune system T-cells & Reduces Proinflammation Cytokines and this HELPS CNS.

7.) Endocrine hormone dysfunction and NonAlcoholic Fatty Liver Disease (NAFLD) leads to insulin resistance, increased inflammation and malabsorption.

article from the Journal of Hepatology June 2006 the European Association for the study of the liver came out with the article entitled "'Endocrine NAFLD' a hormonocentric perspective of nonalcoholic fatty liver disease pathogenesis" by the way this 11 page article had 11 pages of referances to studies backing it up. 

Below is my quoted summation of this article
"The link between insulin resistance (IR), sub-clinical inflammation, Metabolic Syndrome (MS) and nonalcoholic fatty liver disease(NAFLD) is now widely accepted"
2.1 Growth Hormone (GH)
"GH replacement in GH deficient men...reduces levels of inflammatory cardiovascular markers, central fat and increases glucose levels with out affecting lipid levels. These findings suggest a central ORIGIN of MS and, conceivably, of NAFLD."
"in a young patient with panhypopituitarism(condition of all pituitary cells underfunctioning), fatty liver improved, not with hydrocortisone.., but with GH administration."
2.2 Thyroid Hormones
"prevalence of hypothyroidism..with NonAlcoholic Steatohepatitis(NASH that boarders on NAFLD) to be double that of 442 matched controls."
"Studies are needed to ascertain wheather thyroid hormone receptor Beta-specific activation can ameliorate aspects of MS in humans through improved cholesterol metabolism and body weight reduction"
2.3 Adrenal Hormones - 2.3.1 Cortex
"Glucocorticoid EXCESS impairs glucose tolerance primarily by causing insulin resistance (IR)" "these hormones..impair glucose uptake by muscle and adipose(fat) tissues."
"Stress-related chronic hypothalamo-pituitary-adrenal(HPA) axis has been implicated in MS and tissue-selective antagonism of glucocorticoid receptors may be a viable therapeutic strategy for MS"
"decrease hepatic 11HSD1 may PROTECT the liver from glucocorticoid excess." few more sentances are cool too
2.4.2 Androgens
hormones that keep "balance between lean and fat mass and affect glicolipidic metabolism. Hypoandrogenism(under production) in males and hyperandrogenism (over production) in females might thus potentially lead to NAFLD via obesity and insulin resistance (IR)."
"In middle aged men, hypoandrogenism is an early marker for disturbances in insulin and glucose metabolism that may progress to MS or frank T2Dm. Testosterone therapy has accordingly been proposed to treat hypogonadism(under producing sex gland) and to slow/halt progression from MS to its complications"
"Polycystic ovary syndrome(PCOS), a leading cause of infertility, is associtated with insulin resistance(IR) which predisposes the development of MS."

3 Conclusions
"Many endocrine derangements are associated with NonAlcoholic Fatty Liver Disease(NAFLD)." "the liver in patients with endocrine disease and the endocrine derangements in NAFLD should be evaluated systematically."

Me- Is insulin resistance the reason many with Multiple Sclerosis say they seem to do better when they reduce carb intake?  Again these problems are being associated with the liver and hormone dysfunction.
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Note - Realize that a vitamin deficiency is where you are not ingesting enough of a vitamin or getting enough sunlight to activate D3 in your skin. If you get more vitamins this solves the problem.

An absorption problem is when you are getting your vitamins and enough sunlight but are not able to process it and get it to your cells for use.  It is kinda like having leak in your oil line. You can keep putting oil in but until you address the ultimate problem not enough oil is going to get where it needs to and you will have damage done.

I have other data but I think I am making my point that the reason no one causal factor has been found is because malabsorption is due to one or more links in the absorption chain being impaired. Thus, different people will have problems absorbing different vitamins. If this theory is correct it would require everyone get tested to find their specific breaks in absorption and obtain a list of tailor made work-arounds. IE If you can get B12 into your blood but can not break it down to get into the cell then you may need to take Methyl-B12 injections 1-2 times a month for the rest of your life under a physicians care.
Or if your skin has a hard time activating D3 you may need to take oral, sublingual or injections forms of the vitamin D3 for the rest of your life.

If you found this theory thought provoking then please go to your doctor and ask about Getting Tested.