I also suspect iodine was low.
Have you been using iodized salt or sea salt.
You also need selenium, get a multi-vit that lists iodine+selenium and other trace elements.
Cortisol was OK, but could be better. Progesterone may increase cortisol. If you take at night, could help sleep, but if that bumps cortisol, keeps some awake. We know that many with low thyroid function cannot absorb transdermal T products. By extension, I would then expect progesterone and pregnenolone to also not absorb in those cases.
Please be more specific about body temperatures when you first wake up and mid-afternoon.
Food sensitivities or digestive issues.
New house a few years ago? Fumes, mold etc.
fT3 should support normal body temperatures, so we can suspect that rT3 might be blocking T3 receptors. Get rT3 tested.
rT3 can be elevated from:
chronic inflammation or infection - probably allergies or toxins too
Please read the thyroid basics sticky and find references to [using ^F (find)]:
97.3, rT3, adrenal fatigue, Wilson's book, iodine
Your doctor seems to be really good.
fasting cholesterol [can be too low]
CRP - general inflammatory marker
E2 is elevated a bit. If lower, FT could improve.
Problem: FSH/LH are very low. TT and FT should then be very low, but not. This is very strange. Something is wrong with your labs or testes are walking on water!