I had the blood work done....the celiac panel, by a medical doctor. I tested positive on 2 of the tests and negative on the one most specific for celiac.
I went to one of the best celiac centers at a very prestigous hospital and the doctor, who specializes in gluten sensitivity and celiac, told me that there is no way that a stool test can accurately test for gluten intolerance. Furthermore, she said that even if you test positive for gluten antibodies, if the biopsy is normal, there is no reason to eat GF. I felt like you when I ate GF for 2 years. I never felt better...but became more constipated, still have pain, gas and bloat.
You don't have to take this....as I know it's hard to forget the test results...but she is a leading researcher in this area and this is what she says the stool test is not respected by any of the celiac doctors she has ever known.
BTW, I don't know one person who has had the stool test done who didn't test positive for gluten antibodies. Coincidence? I wish we knew if this was really a valid test. I know some swear by it....but it's hard to argue with the experts.
I say, listen to your body. It's telling you it does better with wheat. Or, stay GF for a long time (at least 6 months) to see if your body just needs to get used to the GF diet.