Well, there's nothing like dissecting an epub file to find yourself some rather interesting clues to on what needs to go where, and how. In the process of my picking through the epub, I came across ways to add the missing scene breaks, how to slice up the chapters, and a bunch of other cool stuff. I did figure out too that I can actually use a text editor to create the epub by hand, and then just zip it up, rename the extension, and end up with things formatted exactly how I want them. ^_^
I still don't know all the HTML code elements I need, and I noticed a sid ID at the top of the TOC file I'm still confused about (ie, can it remain the same across multiple files, or does it need to change?) and a few other interesting discoveries. Personally, if I can build all my epubs by hand, I'll have maximum control over how they look, function, etc, which is what I want. ^_^
I think if I get a few more epubs to look at as examples, I might just be able to figure out this whole formatting thing and be able to build them myself with a fair amount of ease.