When I'm translating plain text (Markdown-ish) input to LaTeX, I spend a bit of time going through by hand making sure all my formatting has converted correctly, any accents or non-roman characters are correct, the single- and double-quotes are correct, I haven't accidentally copy-pasted any ligatures, I have included hyphenation for nonstandard words, I've included any relevant non-breaking spaces, figures and headings and captions are flowing correctly, etc. etc. And all of these are still necessary when producing an ebook.
It's maddeningly detail-oriented, but the results are really noticeably much better, and in many cases make the difference between the text being readable and not. It's a bit like the cue dots at the movie theater---if you're not looking for them, you don't notice your uninterrupted experience unless the projectionist screws something up.