Hey tim,
So with the Cross-References going to the wrong page, I can tell you that the reason they are taking you to the next page is that I’m guessing your page marker/anchor is at the bottom of the page, it is being very literal and taking you to the bottom of the page (where your anchor is), which, if you think about it, is the top of the next page. To correct this you will need to place your page anchors at the top of the page so that when you click on a reference it takes you to the top of the correct page.
As far as Endnotes go, I can’t say that I have been a big fan of InDesign’s Endnote feature (which I am assuming you are using?) for epub export. I personally import static endnotes (which you can specify when you import your doc) and do the cross referencing via GREP in the HTML post export. I know it’s not everyone’s cup of tea and it probably doesn’t help with what you are asking, I wish I had a work around for the issue you are having.
Aaron