I'm no expert, but I was just thinking of a few things. It could be a stomach hernia, if you still have pain like that sometimes. I have a hernia that only bothers me for about 4 months when I'm pregnant (just had my 4th). It hurt me, but not constantly. Another thing you may want to try is a really good probiotic. You need to make sure when you get a probiotic that it is the kind that is refridgerated. My baby and I have a thrush infection and have tried to get rid of it for two and a half months. I was on the special diet, and making other major adjustments to lifestyle, and using a probiotic. I thought the probiotic I was using would help, but it was a heat-stable (room-temperature) probiotic and wasn't helping. Just over a week ago I switched to Metagenics brand probiotic in the capsules (needs refridgeration) and I think the thrush is almost gone. I really think it is from the probiotic.
Probiotics and plain yogurt (or Kefir - yogurt drink, can be found at Sprouts) are very helpful in getting the right balance of good bacteria in the intestines and bowels.
Another thought, maybe you have a form of celiac disease and should try cutting out gluten from your diet for a short time to see if it helps. And of course ask your doctor about it.
I know how hard it is to cut sugar, fruits and yeast out of your diet. I don't know how you are surviving while cutting out meat though. I have been cutting out yeast, wheat, gluten, sugar (or any artificial sweeteners of any kind - except Stevia), carbs, and dairy (except eggs and butter). I think that's hard, but maybe not as hard as what you're doing. Basically I can have as much low-sugar vegetables and meat as I want.
Keep up the good fight! I totally understand being in pain and being frustrated at not knowing what the cause is and trying to find answers. Good luck!!