Chronic fatigue, tiredness, general "out of it" feeling, back/flank pain, gerd, ibs, migraine headaches, palpitations, waking from sleep with racing heart, low vitamin d levels, ferritin level of 14, tsh fluctuations; what could this be?

See internist: This problem is so complex that I would urge you to see an internal medicine doctor ASAP. Gluten-intolerance is one condition you will need to rule out but there are also issues which cannot be explained by gluten intolerance alone. I presume you have significant anemia as well. Please keep us update on the findings since getting feedback helps us to do a better job in the future.

No single entity: I don't think any single "syndrome" can cause everything you're experiencing. The ferritin of 14 suggests that your bone marrow iron stores are low & you're at risk of iron-deficiency anemia which can cause fatigue. Thyroiditis can cause changes in TSH levels & may contribute to fatigue & palpitations. A low Vitamin D level in your age is usually nutritional. Discuss all this with your doctor!

Multisystem complain: in patients with multiple system complain ,I suspect underlying anxiety/depression. I will recommend complete check up and also treat anxiety/depression

Multiple issues that: you seem to be addressing w/doctors. Stay in touch w/them. Also, consider a Micronutrient panel to see the nutritional status of your body. Spectracell lab in Texas has an excellent one. Check out their website. Peace and good health.