There is a connection to immune dysfunctions and low Vit D.

So getting that tested is important.

Also autoimmune issues have inflammation present, so using things that dampen inflammation would be helpful.
Fish oil 3 a day (or Krill oil, 2 or 3 a day)
antioxidants, like grapeseed extract, enhanced absorption curcumin, and/or astaxanthin may help. I use 200mg of grapeseed extract for my arthritis and seasonal allergies.

Sometimes there are more than one thing going on. People can have multiple problems.

If you are having fatigue, then supplements that improve energy in the mitochondria may help. R-lipoic acid, acetyl carnitine, and/or the ribose may help that.

Inflammation can be fueled by diet and food choices. So eating an anti-inflammatory diet may help.
You can look up inflammatory indexes on this site of your food:
http://nutritiondata.self.com/

Getting rid of sugars in all forms is a good first step. Increasing insulin in the body increases inflammatory actions. So eating a low carb, high protein, moderate good fats, diet is helpful.