Thought no.1...go check out www.butyoudontlooksick.com. It's for people with chronic invisible illnesses (yes, you count! ) and there are quite a few girls with endo (an endo forum is on the to-do list for Christine I think). If you post in the New Members bit first you'll get some idea of who has endo!
Thought no.2...having a period really &^%$s my tum up, so I can only imagine what endo does. The diet is based on making food easier to digest so it might be a good basis to stick to whatever. How about reintroducing foods according to the diet principles and see how you do. And then reintroducing the occasional bit of dairy or meat later.
Thought no.3....yep, the appendix is near the colon...as are all the girly bits.