I had to seek out a MD that uses nothing but natural medicines to help me with my thyroid & adrenal issues. The practitioner that I was using for healing from the tick-borne infections, while good for that, didn't know enough and wasn't allow to run any tests due to stupid state laws here that allow only MD's to run tests.
Swinging between hyper and hypo thyroid is actually fairly common for someone who's thyroid is really struggling. I would highly encourage you to spend some time doing a bit of reading on:
www.stopthethyroidmadness.com/ Tons of information on this site!!
And it only makes sense for anyone that has been sick for long to have some issues with low functioning adrenals too.