Thank you so much.

You have one gene for Celiac.  You have a second autoimmune disease, Hashimoto's thyroiditis, which is frequently found at a higher rate with Celiac.  HLA genes carry autoimmune disease genes like Celiac and Hashimoto's and diabetes and others.   You have Celiac symptoms of reacting after gluten.  You said "I am however still suffering from the effects of the gluten challenge (food sensitivities, slight brain fog, weird stool, fatigue, swollen thyroid, bodyaches)."  And your anti-thyroid antibodies increase after gluten exposure.  While tTg IgA does not directly attack the thyroid, gluten exposure does trigger the  immune system to produce antibodies against the thyroid in genetically predisposed individuals.  You did not eat sufficient gluten (10 grams of gluten per day for two weeks minimum) to raise the autoimmune antibodies to the point they can be measured in the blood, so your blood tests may well be inaccurate.  You could choose to continue the gluten challenge of 10 grams a day for at least two weeks and get retested.   At the very least, you know that gluten is harmful to your thyroid, and because you are genetically predisposed to Celiac disease, a strict gluten free diet would be beneficial for your overall health.  

Thanks @Scott Adams! I guess my question now is: do the celiacs who can get away with regular contamination without villi damage as you mentioned have to be strict about cross-contamination ? 

Thank you very much @knitty kitty! I'm glad you brought up the point about histamine. I have been taking an antihistamine after meals where I don't feel so good and never knew why it helped so much. At first I thought I might have a food allergy, but I recently did a food allergy test and I actually have ZERO food allergies. Regarding your last point about the stages of grief, are you saying it's likely that I have celiac? I have Hashimoto's BTW and I know for sure that gluten causes an autoimmune response to my thyroid as my anti-TPO and anti-Tg go up and my throat feels swollen. Could the symptoms be due to that autoimmune response?

@Zuma888, The antibodies produced in response to gluten are made in the intestines.  When the body is provoked sufficiently, the antibodies overflow out of the intestines and into the blood stream.  Once in the blood stream, the antibodies can be measured with tTg IgA tests.  Three grams of gluten per day for two weeks minimum is enough gluten to make you feel the symptoms of having been glutened, but the antibodies are not in sufficient quantity to be measured in the blood. Ten grams of gluten per day for a minimum of two weeks is required to get the anti gluten antibodies at a high enough level in the blood stream to be measured by tTg IgA tests. So, no, occasional cross contamination or (heaven forbid) intentional cheat days will not be sufficient for tTg IgA testing.  You will still be making antibodies which will still be causing inflammation and damage to the intestines and body.  Histamine is released as part of the immune response to gluten.  High histamine levels lead to food sensitivities, brain fog, and body aches.   The damage done to the gastrointestinal tract affects the absorption of essential vitamins and minerals.  Malabsorption of fats can cause changes in stools.  Insufficient absorption of vitamins and minerals can cause damage to other organs like the thyroid if it can't get enough Selenium, iodine, iron, zinc, and Thiamine.  Brain fog and fatigue can be caused by low Thiamine and other B Complex vitamins.  Vitamin D is needed to regulate the immune system.  One gene is all that's needed to develop Celiac disease.  I know a Celiac diagnosis is a change that can be difficult to get your head around.  Many people go through the five stages of grief.  One stage is "bargaining".  Sounds like you're stuck there.  Every little cheat counts to your detriment.  But sticking to a gluten free diet, makes every meal a success.   Read the comments below the article... Best wishes!  Keep us posted on your progress!