Ah, the joys of formatting. The notes I took after Tale of the Moone helped, but last night I once again got caught up in just trying to number the pages correctly.
Seriously, I'm not going to say how much time it took.
There's a complicated way to do it, and an easy way to do it. Apparently the easy way I used with Tale of the Moone no longer works. At least, it looks like it works until you actually upload the file.
The complicated way is, well, complicated and convoluted. Of course the examples online don't ever match what is actually on your computer, so you are forced into guesswork, and whenever I did something right I didn't remember the many steps I had taken to get there. And thanks to autosaving, the formatting of my permanent manuscript got messed up, and not even moving it to another file fixed the brand new problems.
Finally I was able to figure out another semi-easy way to do it, and hopefully it will still work by the time book 3 rolls around.
To end on a high note, editing on the print version of The Eightfold Lairs of Xillenthia is done. I will send out for the proof soon, and if all goes well, it should be released within a couple weeks.