So... up till umm 48 hours ago, this is how I made clean EBooks:
* Write in Word for Mac. When complete save as HTML
* Load in To Calibre and fill out Metadata, then convert to EPUB.
* Export from Calibre and open in Sigil.
* Let Sigil run amok with TinyHTML and stuff.
* * Use Find/Replace to remove what is left of Word Dropings
* * Rename file as Calibre makes filenames with spaces
* * Remove cover completely. Add full Res cover back via the "Add Cover" tool
* * Run EPUB Flight Check - Fix anything it finds
* * * Repeat until clean
* * Run EPUB Validator - Fix anything it finds
* * * Repeat until clean
* Remove all prior versions from Calibre and import the new EPUB
* Convert To MOBI
* Upload MOBI To Amazon, upload EPUB to Kobo,B&N, and Smashwords
That process got me good results, but.....
* Write in Word
* Import the .DOC into Scrivener
* * Set Section Breaks (aka Chapters)
* * Compile to EPUB, and MOBI
* Check EPUB against EPUB Validator - Always perfect so far!
* Upload MOBI To Amazon, upload EPUB to Kobo,B&N, and Smashwords
Dang. WAAAAAAAAY better.

I suspect next royalty check that comes in and I am buying Scrivener. The only thing is I am fixing the cover still in Sigil, I need to figure out what setting to tweak in Scrivener to get the cover right, cause it does not get the HTML quite right on it. Everything else about the files is good. I can even tell it to compile a PDF for CreateSpace, but that will wait for my next book to test with. It uses Amazon's official KindleGen for MOBI creation, so that should help with compatibility.
Since I do not write in it, I never thought of just using it for its compile tools.