Baffled by ongoing GI symptoms

I am a 40-year old female with a history of severe medical issues including repeated staph infections, repeated strep and tonsillitis, anemia, headaches, peripheral neuropathy, breast lumps (fibrocystic) and more.  In 2003, I was diagnosed (by blood test) with Celiac but never had the 'gold standard' biopsy before going gluten free.  I responded well to the GF diet and GI symptoms seemed to calm down for a while.  However, I have had terrible problems here and there. I was diagnosed with intestinal parasites about a year after I started the GF diet and felt better for a while after that treatment.  However, starting a year ago, I have had severe medical issues.  In early 2008, I was feeling very worn out and ended up fainting on an airplane.  I hit my head and had a concussion.  My only symptom was a fever.  My doctor suspected Lyme Disease, since I am an avid hiker.  However, tests two months into the illness showed very high Epstein-Barr numbers. Doctors all told me there was nothing they could do. My fever lasted 13 weeks. Then in Sept. 2008, I developed the worst mouth sores of my life.  They started after an accidental gluten ingestion, but continued to spread until I had hundreds in my mouth.  When I was seen in the ER (after 3 different doctors didn't know what to do to help me), they suspected coxsackie virus, but the blood test was negative.  The doctors gave me high dose prednisone and the sores started to go away.  However, when I stopped the prednisone, the sores returned with a vengeance.  So, the doctors kept putting me on 40, 30, 20, 10 of prednisone.  I also had a few courses of antibiotics for various infections that popped up along the way.  At some point, they switched me to colchicine, but it didn't seem to help. A rheumatogist I consulted in Feb 2009 put me back on prednisone, since it was the only thing that made me feel better.  He suspected auto immune disease, but cannot pinpoint one from any of the tests he has run.  My new gastro suspects it's all a rare auto immune disease resulting from years of damage from the celiac.  He is doing another endoscopy and colonoscopy tomorrow to see if there's any evidence of that.  I have had terrible diarrhea since Feb 28th, when I ate at a restaurant (ordered off the gluten-free menu) and got horribly sick at the restaurant.  The diarrhea has only stopped twice... one when I had a barium small bowel series (the barium stopped the D.) and again when I was on antibiotics for a sinus infection.  It's been so severe for the past week, though, that I have dropped 6 pounds in a week.  

Some other symptoms that are ongoing:

Severe diarrhea for 7 weeks straight as of today
Thyroid nodules (just found them in Feb.)
Low Vitamin D Level (I take 50,000 IU once a week now)
Night sweats - very severe - for MANY years  (stopped when I was treated for parasites)
Frequent urination  - get up once or twice a night to urinate
Severe apthuous ulcers
Fevers
Tired
Achy all over
infections a lot
Feeling faint (time to time...fainted on that plane in April 2008, nearly fainted again after flying in March 2009)
Ringing in ears
Multiple Food Allergies (tested positive to 52 foods on scratch tests & blood tests)
Celiac/Gluten-intolerance


Previous:
Whiplash 3 times
Intestinal Parasites 2 times
carpal tunnel syndrome
Peripheral Neuropathy
Molluscum
Staph infections
Chronic Sinus & throat infections
Epstein Barr Virus
Anemia
Celiac or Gluten Intolerance
Ovarian Cyst


My new doctor suspects some sort of rare auto-immune disease and is suggesting some old chemo drug called mp 6 (?).   My sister thinks it's my gallbladder.  I have a history of serious  auto immune disease in my family, as well as a history of colon cancer and parkinson's disease.    I should also add that my epstein-barr numbers are now normal and that the doctors have checked for vitamin deficiencies and just about anything else you can think of.  My immune system function seems a little low and vitamin D is low (was 20, have brought it up to the 40's). Other than that, everything fits 'normal'.  

Does anyone have any thoughts?  

kat