Joyous-
I can relate to your tummy woes. I started vomiting, even upon waking in the a.m., in November 2006. I went to my family doctor, who thought it was a virus. I returned a couple of weeks later and was given antacids. Mind you, I didn't really have much in the way of nausea and felt fine after vomiting.
I was finally referred to a gastroenterologist who did a colonscopy, endoscopy and finally, a gastric emptying study. They determined I had slow stomach motility (gastroparesis). I finally saw a motility specialist who determined that the nerves in my stomach aren't working right and not making contractions strong enough for the food to digest. Also, my stomach is not stretching, so it can't accommodate food like it used to.
When I tired of vomiting (because my bladder grew weak and I was peeing on myself at the same time

), I went on an all liquid diet (Ensure). I slowly began eating solids again. I have "flares" every few months where I routinely vomit after eating and even today I can't keep a meal down if I've eaten to much. Kinda like gastric bypass without the surgery

Although I had only previously experienced a tad of heartburn with my third pregnancy, I developed unbearable heartburn in the Summer of 2007. In retrospect, I think it was my body "flaring" from autoimmune issues at that time--the tummy's where it attacked.
I honestly believe that my tummy troubles are due, in part at least, to the lack of saliva I produce. I have VERY little saliva (<.1 ml after 1 minute), therefore, there's nothing to help the food move in to the stomach and assist in the digestion process. I have to be really careful of the texture of food, because if it's really dry (like toast) and I drink water with it, I will vomit because I've eaten/drank too much for my tummy to hold. Before I received the SLE and SjS diagnosis in December 2008, I couldn't understand why when I vomited the food would feel "stuck" in the esophagus. Although I'd had a dry mouth for years, I thought it was related to medication or just not drinking enough liquids, not an AI disease.
Remember, this is purely my situation and theory and your situation could be totally different. I'm just trying to offer some insight as to why you might be having digestion problems.
Please keep us posted on how you're doing