Was your thrush due to an antibiotic? Have your doctors done blood work to make sure whatever medications you are taking for the autoimmune disease isn't weekening your immune system? Immunosuppressants will do that. Your cursed for being sick all the time anyways, with autoimmune disorders. I'm sorry, I know the feeling.
Sounds like you need to see a gastroenterologist. Maybe you should have a test done to check for gastroperesis, and maybe an endoscopy/colonoscopy. I would definetly check into getting a referral to a stomach doctor if you don't already have one.