I'm sorry - it's hard when your doctors don't know what's going on. Hopefully they'll figure it out soon. (((hugs)))
If you are exhibiting a lupus rash, it's probably good that they are taking you off the Remicade, because remicade is known to sometimes cause a lupus-like syndrome.
Do you have any blood in your stool? If you have iron deficiency anemia, you probably need to supplement with iron, or get an iron infusion. Also, get your B12 levels checked, if you're deficient in B12 (and it's possible if your terminal ileum is inflamed), they can give you shots of B12, which should make you feel better (at least it'll help lift the anemia related fatigue). Hashimoto's is linked with anemia . . . so that could be the other reason for the anemia (taking iron, folic acid and B12 should help with this - my mother has hashimoto's and she would be anemic if she stopped the regimen of folic acid, B12 and iron supplementation).
Also, a high platelet count could be because you are bleeding somewhere (perhaps the ulcers in the small intestine). Platelets help with coagulation (body's mechanism to try to stem the bleeding). When my husband was in the hospital, with nothing but bloody diarrhea, his platelet count was through the roof. Once his bleeding was under control, the platelet count came down to normal.
Have they done an upper endoscopy? They should be able to collect biopsy samples, which should help figure out if you have crohn's, and how severe the inflammation is, and also if you have any stricturing. It sounds to me like they need to do more diagnostic procedures to figure out what's going on with you. Also, there is a prometheus labs test that looks at genetic markers (I think) to see if you have a predilection to crohn's disease.
While not being able to pinpoint the exact autoimmune disease that is causing your problems is not so great, one good thing is that if they are at least certain it is autoimmune, most autoimmune diseases have the same treatment options (steroids, immune suppressors like 6-mp, imuran and methotrexate, and anti-tnf agents like Remicade, Humira and Cimzia). Perhaps steroids will bring down your symptoms, while your doctors try to figure out what's going on?
Hang in there. Hope you get answers soon.
Husband with Crohn's
Diagnosed March 2003 Ulcerative Proctitis
Diagnosed March 2008 Crohn's & C-diff, hospitalized 45 days
Canasa, Lialda, Remicade, VSL#3, Florastor
In Remission since June 2008
Stopped vancomycin for c-diff Jan 1 2009
C-diff free, until Sep 2, 2009
Fighting c-diff, I guess for life