I am quite fond of the three molecular biology courses from MIT on edx [1][2][3]. Not only are the lectures great, but they also have spaced repetition built in. The exercises are often great counterfactual questions that encourage deep understanding.
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.
[1] https://www.edx.org/course/molecular-biology-part-1-dna-repl...
[2] https://www.edx.org/course/molecular-biology-part-2-transcri...
[3] https://www.edx.org/course/molecular-biology-part-3-rna-proc...