I did follow up on the question about when to take Cortef in relation to the time of blood draw for tests. Through the help of an online lab testing company they got an answer from a doctor that Cortef should reach its max effect on serum cortisol levels in about one hour. Cortisol has a circadian rhythm by which it is normally highest at about 8 o'clock in the morning and drops off over the rest of the day. I think the best info you can get from the morning serum cortisol test is your cortisol level (including the Cortef) at about 8 o'clock in the morning. If you defer the morning dosage, the test would only show the residual level from prior day.
Also I wondered what amount of Cortef you are taking and at what time of day?
From your thyroid tests your Free T4 is lower than optimal for many people, which is mid-range, at least. Your Free T3 is at a good level, but since you still have symptoms it also makes me wonder about your Reverse T3 level. Reverse T3 is a normal product of conversion of T4 to T3, but in the wrong situation, it will be higher than optimal. Since Reverse T3 blunts the effect of Free T3, it is reported that the ratio of Free T3 to Reverse T3 should be at least 1.8. So I think it would be a good idea to test for Reverse T3, along with Free T3 from the same blood draw.
Vitamin D should be a bit higher, at least 50, B12 should be in the upper end of the range, and as I understand it, your cortisol is lower than it should be at that time of day. I have to qualify that by saying that I don't know the effect of deferring your Cortef until after blood draw. I will do some reading on that.
Sources say that thyroid and cortisol need to be in a reasonable balance. There are also sources that say raising Free T3 med when cortisol is low will cause reactions. And I know that low cortisol will cause lots of muscle aches and pains. Your morning serum cortisol test is total cortisol, which is not as revealing as free cortisol. I would ask the doctor about a diurnal saliva cortisol (free cortisol) panel, which consists of 4 tests taken at different times during the day. It will show your cortisol status much better. If the doctor resists, you can order a kit online at ZRT Lab and get that test panel done for about $145. Even then you would have to get the doctor to accept the results and respond accordingly.
For hypothyroid patients it is important to make sure that cortisol levels are always adequate. As I understand it in time of stress, cortisol med dosage should be increased a bit. So I would talk with your doctor about additional testing for cortisol and also the possibility that you need to increase your dosage. Also I suggest testing for ferritin and if needed, supplement to optimize to at least 100. Although you likely need a change in your thyroid med dosage, I would not recommend any change until after getting these tests done.
I don't think that 15 mg of Armour, which is only about 10 mcg of T4 and 2.25 mcg of T3, would be the cause of your muscle pain. That just doesn't compute. So let's try to look at the full picture. Please post your most recent thyroid related test results and reference ranges shown on the lab report. Also, if tested for Vitamin D, B12, ferritin, and cortisol, please post those results and ranges as well.