Your double TOC problem may be solved by
the same method this guy is using, though that seems unnecessarily complex.
I find that the best method for me is to take or make an ePub and then convert to mobi. And I only edit my purchased/downloaded books to fix the formatting and correct any really noticeable typos so they aren't too horrible to read on my Kindle.
ePub is really just a set of zipped up mostly html files that you can easily change as needed. If you need to change just one thing, then you usually have to just change one file. Whereas mobi is a specially compiled binary file that you'd have to uncompile and redo and reassemble every time you wanted to change anything besides the metadata, and as your words about MBPC (which I have never used) suggest, you have to redo even the metadata from scratch whenever you re-create your book.
In the future, I would advise going from your filtered Word document to creating an ePub in Sigil, and then using KindleGen to convert the ePub to mobi. You may have to make two versions of the ePub; one that keeps the formatting to Mobi's more limited display capabilities, and the other that can take full advantage of greater supported features of ePub.
But ePub is significantly easier to work with and alter directly, even if there is a bit of a steeper learning curve to get the workflow set up and understand how it works, I think it definitely pays in time and frustration saved in the end.
In any case, for your existing book you can use Calibre to convert your mobi to ePub and then edit that in Sigil, but sometimes that produces extra formatting markup in the source which you may not need or want,
such as this guy found he had.