If your source files are .html files, you should give
Sigil a try and create an ePub first. (The latest Sigil version features a spell checker, enhanced search and replace functions and it can also automatically generate a TOC from header tags (<h1>, <h2> ...)
Once everything looks OK, you can then convert the ePub to mobi with Calibre, which will add a Kindle inline TOC.
Since Sigil is a WYSIWYG editor, your mobi book will look pretty much like the ePub version. I.e. no more unexpected font size issues.