If I were you i would look into clearing, cleaning and re colonizing your gut. This is what i do with my clients. Many of them suffer from multiple auto-immune issues with varying causes. From hoshimotos, tied to celiac or crohns and then clients with sibo and the other 2 conditions.
The process of clearing the gut is different in each case, but once the gut is cleared, the process of cleaning/repairing the villi of intestinal tract is pretty much the same. A mix of insoluble and soluble fiberous foods must be reintroduced into the diet. For steps 1 & 2 probiotics are to be avoided.
To give more help I'd need more on your exact issues, but I hope this helps you to solve your issues.