I am doing something similar. One way to go about it is:
- Create a specially formatted HTML file with your book (see info on kindle formatting guides below); and
- Use the command line Amazon KindleGen tool to generate the eBook.
As far as creating things like the Table of Contents, starting chapters on a new page, and other things that can be accomplished in a Kindle eBook, you may want to read a kindle formatting guide, such as the Amazon Kindle Publishing
Guidelines.
Also, you may want to read a book by a third party on the subject. I have personally read Kindle Formatting by Joshua Tallent and How to Format Perfect Kindle Books by Steven Lewis and they both contain the information needed for properly formatting a kindle book using an HTML file. You can obtain both books from Amazon. The Tallent and Lewis books are aimed at authors that may have never created an HTML file by hand and guide you thru the process.