Goodness Brightlight You certainly seem to be doing some reading! Great to try to understand what's going on in your body and sounds like you would benefit from studying human biology!
As you've found out our endocrine system functions less well as we age - as with many of our bodily functions. here is an summary of hormonal changes with ageing:
http://www.nlm.nih.gov/medlineplus/ency/article/004000.htmAnd of course there is the wonderful interaction and influence of mind with body and body with mind so that - in terms of chicken and egg - it is both. Our mood is most definitely influenced by our hormones and oestrogen levels have a profound and direct effect here (and I think testosterone too?). This is what fluctuates and then decreases so dramatically at menopauses and gives rise to the bewildering myriad of symptoms that women experience.
The other way round also has a profound effect as you mention Brightlight - ie the negative effect of stress - through external factors - on our physiology and some hormones, and eventually our general health.
For those who don't have the time to grasp how all this works, and the complex mechanisms - then this is the time of life to try to reduce all the current stresses in your life, concentrate on general health and well-being - through diet, exercise, and control of weight, alcohol and smoking, to look for non-chemical ways to cope with hormonally induced anxiety - the best way to improve adrenal function - and to look at replacing the hormones which become deficient, if you are medically able to do so - ie oestrogen.
Regarding the adrenal glands - the concept of adrenal fatigue is not a recognised condition - and I think originates in US where they have a different health-care system and may well be linked to a product you can buy that claims to cure adrenal fatigue?! There is a rare disorder of the adrenal glands called Addison's disease - but it is unlikley that any of us suffer from this - as far as I understand adrenal function is not one of the standard tests on NHS except for individuals that could be suspected of this?
In terms of progesterone and the adrenal glands, from what I understand all the steroid hormones that are produced by the adrenal glands orginate from cholesterol and the production will balance itself through homeostatic mechanisms. Not sure where the idea of depleting progesterone comes from in this context but it is important to distinguish between the hormones produced by the adrenal glands and those from the gonads ( sex organs). Men and women produce progesterone - I think in the adrenal glands - in small amounts throughout our life including post-menopausally, which is responsible for a number of functions - I don't know all of this and not sure if it is yet completely understood?
The progesterone that we mostly refer to in our menopausal discussions is produced during the menstrual cycle (before fertilisation) by the corpus luteum ie the empty egg follicle after ovulation. The amounts are huge compared to the amount produced by the adrenal glands. It is this that decreases at menopause - because it is no longer needed for pregnancy, and depletion of this is not related to cortisol or the adrenal glands but the menstrual cycle and ovulation.
I realise the whole subject is extremely complex and there are different physiological processes going on but just wanted to highlight these points!
I don't know why thyroid function in particular seems to be affected in many women as we reach this age. This isn't explained in the link I gave - and haven't yet looked around for a biological explanation from reputable scientific/medical site!
Hope this ramble (really me thinking aloud) is of some interest to someone!!

Hurdity x