I'm glad you checked out Stop the Thyroid Madness. You mentioned having your doctor check your cortisol. What I did was use a 24 hour saliva test. You take samples throughout the day. That's more useful than a one time cortisol test. You need to know your cycle throughout the day.
I hope you find the info on STTM helpful. There's also a facebook discussion group that I found very helpful in the beginning of changing from Synthroid over to dessicated thyroid.