Sounds like your Autoimmune is affecting your GI tract. I recently have been diagnosed with HYPO-CONTRACTILE Esophagus disordered brought on by an autoimmune disease (either Lupus or Scleraderma) I have yet to find out which. I had persistent acid reflux that worsening. I went thru multiple testing including a esophageal motility test. That confirmed my diagnosis. I am still trying to piece it all together. My mother had Scleroderma. I would search out a Gastroenterologist who is willing to treat the patient as a whole patient not just the GI tract.