OH dear... I see far too many similarities in your statement.
I have both. I've been seeing a ND for both since Feb with remarkable results. But anyways, to answer your first question. Endo and PCOS are generally causes by your horomones being out of balance. Theres no "specific" area to pin point, but women with either, or both, have massive horomonal imbalances. The BCP's force your body to have certain horomones are certain times. For some people, this helps with pain and issues, and, IMO give a false sense of security.
Alot of what I say is my own theories, Im not a DR, nor a ND. Although alot of my thoughts are based on my conversations and research with both. Your liver has alot to do with your body's horomones, as it cleanses out the excess, and regulates as well. Im currently on some naturalties (ok I made up that word) to cleanse and boost my liver function. Before March, I hadn't had a 'real' period for almost a year (not including the BCP mayhem I went through sept-jan). I've now had 2 periods since march, so I think Im on a roll!!
BTW, when I first was on my road to discovering my Endo, they said it was IBS--I'll have you know now, with my treatment, 90% of all those isues went away nearly immediately.