Sorry that you are still having stomach problems. One other thought is that it is another food. Sounds like you react to soy . Other foods that commonly cause problems are yeast, corn, nightshades, legumes, eggs. Of course any food can be a problem, but these seem to be amoung the common ones.

I react severely to gluten and yeast. I test positive to casein and eggs but don't seem to have a noticible reaction to these. It is rare that I will eat dairy or eggs.

As Cara said, it may be that your stomach needs more time to heal. B12 can also have a healing effect on the stomach. Are you on B12?

I cannot find a GFCF chocolate that doesn't have soy lecithin but I have heard that there is no soy protein in soy lecithin. If that is true, one candy bar that would be ok is Tropical Source Rice Crisp. A search for GFCF chocolate will bring up some sources on the web.
Anne