Calibre will create the book in zip format.

(d) Click 'add book' button in Calibre and select your 'Table Of Contents' file. On the 'Table Of Contents' page tick 'Force use of auto generated Table Of Contents and Do not add detected chapters. Untick everything in the 'Heuristic processing' and 'Structure detection' pages. (d) to set up calibre, go to 'preferences' => Common Options. Just change its html title and header and see what happens.) If other files refer back to this file, see if you can just use the original parent file without changing its file name as the 'Table Of Contents' file. ( I am assuming this file is the parent to all links. If needed, make your additions to the links in this file. Change (or make one if there is none) the first header to h1>Table Of Contents. Edit it and change title to Table Of Contents. (c) Take the site map or index or whatever page that does the best listing of what's in the web. (if the web has an index page or site map listing the pages, your job is easy.) This will create a browsable mirror of the web site on your local device. (b) spider the web site: Cyotek WebCopy or HTTrack Website Copier will do just fine. Then you convert the zip to ebook in Calibre.

(a) for the conversion to epub use Calibre. Then it turned out to be ridiculously simple. Developed mile long Xpath strings and what not.

Mobi file