What I've learned:
1. Command line programs are not my friend. This was what brought me down to crashing defeat in my attempt to completely build an e-book by hand. The very last step is to compress all the different files into a zip file, using a command line zip program because there's one tiny little line of code in its own file that has to go in first and end up at the very top of the zipped file. I followed the instructions exactly, but I just couldn't get that bugger to go in right. I'd run the program, compress my files, run it through the epub validator, and keep coming back with just that one little error. And that one error, that one little 20-byte file, made the ebook unusable. Otherwise it was perfect. *sigh* So I backed up and used the very beautifully-written html and css that I came out of the process with, and learned my next lesson:
2. CSS is my friend, and I can do it. I'd been trying to learn CSS for years and could never quite grasp it, but for some reason the way it's laid out in The eBook Design and Development Guide by Paul Salvette clicked for me. Following the instructions in the guide (and applying the principles to adjust a few things, like my smallcaps, that weren't working right) I ended up with html/CSS files that converted beautifully when I did find conversion methods that worked for me. I'm proud of the formatting in my ebooks, and I hope it leads to a more pleasant reading experience for the readers. Even if the novel isn't great, at least the formatting is wonderful.
3. Also from the eBook Design and Development Guide: Regular expressions are awesome. These are things you can do in a text editor like Notepad++ to do fiddly tedious little things like strip extra blank lines and spaces from a file, wrap the correct html tags around paragraphs or sentences, and cool stuff like that.
4. The CreateSpace Word templates are crazy-making, The formatted one came with weird sections and headers that didn't fit with my novel and that I couldn't figure out how to get rid of. The un-formatted one ate my dropcaps. Finally (after an equally frustrating foray into LibreOffice [see below]), I just set up my own pages using the margin guidelines on CreateSpace, and that worked fine.
5. LibreOffice has many advantages over Word, but its developers hate page numbers. Setting up different page numbers for different sections and getting the right numbers in the right place is much easier in Word. (Or maybe that's because Word's instructions are better-written.) (Note that I'm using Word 2003. Can't speak for later versions.)
6. Typing out small caps for each different version is a pain. Do it once on the source file before doing anything else.
7. Smashwords' Meatgrinder converter actually does a really nice job of converting your .doc into various ebook formats if you follow the Style Guide exactly. I'd heard lots of complaints about the Smashwords conversions, but I'm very pleased with how mine turned out.
And some things that may remain mysteries forever:
1. Why did Sigil make my epub come out with a humongozoidal cover image? Seriously. I looked in the previewers, and got a friend to look at it on her Kobo, and you could only see like the top left quarter of the image. Running the conversion through Calibre resulted in a correctly-sized cover image.
2. Why do the makers of LibreOffice hate page numbers? And who writes their instructions? Seriously, that isn't something that should be so hard.
So there's two weeks' worth of lessons that should reduce the formatting, conversion, and publishing time on my next book to two days.