What kind of doctor should i see if my general practitioner thinks i may have an autoimmune disease or multiple sclerosis?

Depends: If indeed you have one of these, they are handled by quite differed specialists. Autoimmune diseases are usually handled by rheumatologists while multiple sclerosis is usually handled by neurologists. Some actually specialize in each category but early disease can be handled by general internists.

Neurologist: I would suggest starting with neurologist if ms is a major consideration.

Neurologist: If you have symptoms afflicting either the central or peripheral nervous system, see neurology. If involvement of joints, can see rheumatologist. MS is just one of many diseases which are mediated via autoimmune mechanisms.