Usually, I don't go through any of that. When I convert anything to ePUb, be it PDF, RTF, Lit or HTML, I'll usually put the ePub in my ITunes and copy to my IPad. IF it doesn't look good or no Content's what-so-ever for chapters, I'll just open up Sigil and add the chapter code into it. Pretty easy when you get used to it.
Usually takes me 30 minutes to make a garbled PoS book look like it was made for the IPad lol