Help with High Cortisol Levels and other hormone issues

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I am wondering if anyone can help with some of my recent tests. Here

is a little background on me. I was on Depo Provera on and off for

about 6 years. After I got married in 2003 I stopped taking the shot

and that's when my health took a turn for the worse. I then went 2

years without a menstrual cycle and saw about 5 different doctors and

none could tell me a reason for all of this other than I had extremly

low hormone levels (progesterone & estrogen). I have been checked for

PCOS about 5 times and nothing really checks out with that - I have

maybe one symptom out of the myriad that you can have. Anyways - long

story short I finally got my cycle back using natural hormones about

1.5 years ago. Still after all this time I have never felt really

normal. Always tired, gaining weight (even while eating a good/strict

diet) working out, taking vitamins etc.

Finally I was able to get my thyroid checked again last fall and was

put on Armour thyroid. I have now worked my way up to 3 grains as of

Jan and was feeling pretty good. Then after my new doctor switched me

from sublinguals to creams (hormones) I started to feel worse. I

gained weight immediatly, felt aggitated, hot and bloated. After

reading online about Progesterone dosages I am now thinking I was on

too much. He had me taking 200mg per day. Does anyone know if this is

way too much? Also, he took my salivia adrenal test and it came back

with HIGH cortisol levels at 3 out of 4 points during the day. Sorry

this is so long already but here are my questions and test results:

1. Can taking the progesterone cream at 200mg for 2 months cause my

cortisol levels to rise that much? If so, what should I be taking to

get them down and does anyone have experience as to how long this

process might take?

2. Is my thyroid function being affected by this high cortisol?

3. I would love to get pregnant sometime this year but sadly do not

think I am ovulating at this time (using a fertility monitor daily).

Is there anything else I could be doing to help with all of this?

Here are my latest adrenal tests:

7AM - 1.59 (0.27-1.18 mcg/dl)

11AM - 0.88 (0.10 - 0.41 mcg/dl)

3PM - 0.26 (0.05 - 0.27 mcg/dl)

10PM - <0.03 (0.03 - 0.14 mcg/dl)

My latest thyroid tests were only on 2.5 grains. I have since gone to

3 but here they are for reference:

T4 Free: 1.0 (0.8 - 1.8 ng/dl)

T3 Free: 330 (230 - 420 pg/dl)

TSH: 0.19

I am waiting to get my other hormone tests back. We just drew a Day 19

Progesterone test and I will do a Day 3 Estrogen after my cycle comes.

I guess I am just so confused at this point and not sure what to do. I

would really love some advice from all of you.