Lyme can affect thyroid, adrenal, and hormone levels. I have posted many times that I feel it is very important for anyone with Lyme to have all of these levels tested. When they are not optimal, it can cause many symptoms.
It is also important to see a doctor who is knowledgeable. In my experience, there are not many. I have had the best result by calling a compounding pharmacy in my area to ask if they can recommend a thyroid doctor and a doctor who can treat adrenal and hormone imbalances. These doctors often use compounding pharmacies.
For thyroid testing, be sure to get the Free T3, Free T4 (besides the T3 and T4) and thyroid antibodies tested in addition to the normal panel. These are simple blood tests. They are not usually done but are necessary for a comprehensive view. It is my understanding that saliva testing is more reliable for adrenal and hormone testing than blood tests. My doctor used ZRT Lab for testing.