Absolutely regarding the menstrual problems and liver, and the thyroid problems and liver! The liver processes estrogen (a very toxic substance until processed) and makes T4 (I am no expert, but I have read this).
And yes, you can get liver pain from congestion. Try a castor oil pack right away for relief, it's very gentle and "safe". You will have to read up on liver flushing, enemas, and coffee enemas to get futher along in your healing journey (Andreas Moritz book). But I believe you have come to the right place to start. It's a long road for some, but nothing the MD can do will help you heal this, IMHO, so take control of the situation and start learning and healing yourself, you can do it!
Check out the recommended messages on this forum for more immediate guidance. Also, you are on a high fat diet, probably because you can't tolerate grains from liver congestion/dysbiosis so you have adopted the paleo philosophy. Please keep an open mind regarding what your body needs at the moment. I didn't start to begin to heal until I adopted a high carb vegan diet for example.
I wish you all the best but don't even wrestle with the idea if all of your health issues are connected to the liver, posters here will wholeheartedly testify that they most certainly are!
Wishing you healing today:)
p.s. colonoscapies are not risk free, fyi you will most likely be doing colon cleansing to get well