Hi Bella. Lyme disease can affect all hormone levels. Many symptoms of hormone deficiencies can overlap with Lyme disease. As I have posted many times, I believe everyone who has Lyme should have their hormone levels tested.
Regarding thyroid testing, it is important to have the Free T3, Free T4 (besides the T3 and T4) and thyroid antibodies tested in addition to the normal panel. They are not usually done but are necessary for a comprehensive view. If antibodies are present, it can indicate Hashimoto's Thyroiditis which is an auto-immune thyroid disorder. It is fairly common. If you have Hashimoto's, your other results may be in the normal range but treatment is warranted.
Regarding adrenal and hormone testing, from what I understand saliva testing is more reliable than blood testing. One lab that does saliva testing is ZRT Lab http://www.zrtlab.com/default.aspx?s=1 This lab can test cortisol, progesterone, estrogen, testosterone, estradiol, and DHEA levels.
One book about adrenal fatigue is "Adrenal Fatigue, The 21st Century Stress Syndrome" by Dr. James L. Wilson. Adrenal function is also discussed in "The Lyme Disease Solution" by Kenneth B. Singleton MD.
I hope this helps.