I am so sorry to hear that you've been through so much this year. Especially about your job being unwilling to accommodate you. Did you know that Lupus falls under the Americans With Disabilities Act? This act states that your job must provide accommodations if you are found to be disabled.
" The ADA requires employers to provide reasonable accommodations for employees who have a disability, including lupus, so they can continue to perform their job." You can call the ADA and talk with a job accommodation specialist.
Another source is The Job Accommodation Network (JAN) at askjan.org is a free service of the U.S. Department of Laborís Office of Disability Employment Policy. A JAN consultant can talk with you about your limitations and help you brainstorm accommodations that may work for you. The consultant can also coach you on how to talk with your employer about your disability. I am not sure if this will help you retroactively, but it might be worth it to find out.
I do hope that you and your doctor are able to get you approved for disability. Prepare yourself for the fact that, quite often, they arbitrarily deny initial requests in the hopes that you will not pursue the matter further. It is very unfair, but they've done it to many people.
I'm glad to hear that your primary is working with you and doing what she/he can to help you. I hope that you get appropriate treatment very soon, that your disability is approved, and that you can reduce your stress in order to take care of yourself. I wish you the very best.
Peace and Blessings
Look For The Good and Praise It!