You say it didn't work but now you're asking about different problems...
For the chapter header sizing, please note that Mobi is extremely limited in it's styling capabilities. It's possible your 1.2em style isn't large enough to get translated to something heavier weight in mobi. Generally best practice for any document is to use <h1>, <h2>, or <h3> tags instead of <p> tags around chapter headings. I realize that's probably not news you want to hear. What you could try is editing the css to make it larger than 1.2em and see if that helps.
Regarding the duplicate inline chapters, that's expected behavior, several links to read up on that:
http://www.calibre-ebook.com/user_ma...-in-mobi-files
Solution:
https://www.mobileread.com/forums/sho...0&postcount=11
https://www.mobileread.com/forums/sho...d.php?t=129364