If you are already accustomed to Calibre, you could give a try to its full fledged [ebook editor][1], that handles both `epub` and `azw` formats.   
Having the source HTML files, it should be an easy task to import them in the editor and create the ebook, complete with a proper table of contents.

[![enter image description here][2]][2]

Some other related questions:   

 - [How to build an epub starting from a bunch of HTML files?][3]   
 - [Are there any WYSIWYG editors for EPUB books?][4]

  [1]: https://manual.calibre-ebook.com/edit.html
  [2]: https://i.sstatic.net/TqC7G.png
  [3]: http://ebooks.stackexchange.com/q/294/136
  [4]: http://ebooks.stackexchange.com/q/132/136