Well, I have lots of clues, just not the knowledge you have.
Here's my frustration: I use Word 2010, saving everything in Word 97-2003 format, using styles for everything. You won't find tons of garbage because of this (no big areas of white space and long rows of page breaks). Using MobiPocket, I create PRC files that, after being converted by Amazon to AZW, display PERFECTLY, as intended, on every single Kindle device in use. No loss of em dashes, no screwed up ellipses, no inconsistent line heights in a single book.
EPUB, it turns out, is a whole different ballgame. It isn't a friendly playing partner with Word, which I suppose is why you have such a distaste for Word.
Hell, I'm anal enough that if I thought re-writing everything in Sigil would help, I'd do it. I'm a perfectionist, enough so that if I were 100% certain that Sigil would preserve my intended formatting, I'd be all over it.
I tried using Sigil for this current project, using tips given by an author on the Web, and it didn't work out. I've had to settle for what Calibre will give me.
If anyone would like to see my Word or ePub files, I'd have no problem sharing them. The book has long been published on Amazon and in paperback that I wouldn't worry of thievery, not that anyone would try.
All that aside, I am convinced the Simple Touch has a lot of display faults.
I'm willing to learn. I'm not in love with Word. Writing a book in HTML, though, especially fiction, seems quite a chore, one that would definitely stem creativity. But if there's something I'm missing about your method of writing, I'm all ears, my friend.
Thanks a lot, you guys!
Greg