[jplatzek]

Biologist here. I would start with a textbook called Janeways Immunobiology. It is the textbook that all of us have used to learn immunology and should be accessible for anyone with a high-school understanding of biology. The book already has many explanations of autoimmune diseases, so it should be everything you need.

[ashtonbaker]

Seconding this. I would also add that Biochemistry was really the class that first gave me the "I should have loved biology" feeling, so whatever the equivalent Biochem textbook is might be interesting as well.