Please keep in mind that an accurate medical diagnosis cannot be provided as I have not personally examined you nor reviewed your history and workup. However, it's safe to say that it is very unlikely that you have Hashimoto's encephalitis as this presents with severe, progressive neurological signs/symptoms over a period of weeks that in many cases culminates in a decreased state of consciousness, not just some problems with confusion and attention. Many of these people are in a near comatose state, with seizures, myoclonus, dementia, and psychosis as part of the picture. ANd of course, the thyroid levels are abnormal.
In contrast, your symptoms have been going on for quite some time and do not appear to include the profound neurological deficits I mentioned above. If you are unsure of the diagnosis of MS, other testing can be done to confirm it such as evoked potentials and a special tourtellote's study done on the CSF that measures immune system products. Blood studies for lupus, B12, and other autoimmune diseases such as lyme and sarcoids can also be considered depending on the clinical suspicion for other diseases. Unfortunately, MS in itself is well known to cause cognitive disturbances. Talk to your doctors about your questioning the diagnosis and have them explain what they're thinking is. If you are still unsure, consider a second opinion at a major academic center. Here at the Cleveland Clinic, we have the Mellen Center which is a specialized comprehensive clinic for MS patients with experts in the field who can help you figure things out if you are nearby. Good luck
Encephalitis Global http://groups.msn.com/EncephalitisGlobal offers information and support to people touched by all types of encephalitis. I believe that (at least) two of our members have mentioned Hashimoto Encephalitis.
I sincerely suggest you await feedback from the medical professionals who are attending to you. If you seek conversations with others, I hope you will stop by Encephalitis Global.
Wendy - encephalitis survivor
Vancouver Canada