For anyone still following along I read this article which briefly explains the gut - thyroid connection.
http://drhedberg.com/2011/02/15/the-gut-thyroid-connection/
The theory I'm currently considering:
Overtraining and calorie restriction drives up my cortisol and RT3 resulting in lowered immunity and low body temperature. Some form of dysbiosis / candida etc (don't know enough about them yet) starts spreading in my gut which would normally have been killed off at a normal body temperature with normal immunity.
They precipitate continued impaired conversion of T4 to T3 as explained in that article and continually disrupt proper absorption of nutrients resulting in continued lower immunity, hence the continued sinus problems I have been having. Now the dysbiosis remains despite good diet / no training / lots of sleep and hence me possibly chasing the wrong stressor in the overtraining, which is obviously no longer going on now.
The question is how to remove it iif it is there? One option,I am theorising, is just to use T3 for a time to increase body temperature to normal, removing the right envorinment (low temperature) for it to live.
There are of course pro biotics, things to 'heal' the gut wall, elimination diets etc but I'm not well versed in any of them. (I'm obviously not particularly well versed in T3 or the thyroid either, but its what I've focused the bulk of my research on along with the rest of the endocrine system)
I guess that is why we employ the experts, looking forward to getting matrix take on it in my consultation.