It's very common for people with autoimmune disorders to have low Vitamin D - though as far as I know, nobody really knows WHY.
I'm sure others will reply, but I was on 50,000iu per week for about 6 months to get into the "normal" range. It's very difficult to get your levels up adequately with non-prescription supplements.
I definitely felt better after my levels were up...the Lupus didn't go away by any means, but I had a bit more energy.
Hope that helps....