What type of book are you publishing? My suggestions will be very different depending on how complex the structure of the book is and how graphics intensive it is. Publishing a graphic novel is very different from publishing "8088 Assembler Coding for Fun and Profit" which is very different from publishing a YA Urban Paranormal Lesbian Romance Fantasy novel.
Are you using this as a learning experience? If not, just pay someone to handle the formatting for you. If you are an experienced developer, your time is worth more than a good formatter's. I can recommend some good formatters.
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