Non-ascii doesn't work well (at all?) with rtf. It sounds like you've tried a lot of different things, not sure if you've followed these steps.
- Open in Word
- Save as 'Filtered HTML', use UTF-8 as your encoding.
- Add the HTML to Calibre and convert from that
pdf problems would be completely unrelated - it's probably something wrong with the pdf. Open a bug at bugs.calibre-ebook.com with one of the problem files.