Basically you'd have to export out to HTML (Mobipocket is really just a modified HTML 3.2 that's compressed) edit out the bits you don't want, and convert it back to Mobi again.
I actually recommend making a proper ePub file from your extracted text and converting that to Mobi. Easier to edit again later without having to go through the entire process all over again.
You can use any number of tools for this: Calibre,
MobiPerl, or
Mobiunpack (all created by MR forum members, with support threads) to extract, your favourite text editor or a specialized tool like Sigil to re-create the book you want.
And then use Calibre, MobiPerl, or Amazon's
KindleGen or
Kindle Previewer app (these last require an Intel Mac w/10.5 or better) to create your new Mobi file (under KindleGen, use the -c2 setting for tightest compression, and the
KindleStrip python script to get of excess bloat).
Incidentally, if you have access to an ePub or even HTML source for your books, it'd be best to start from that. Tidier and simpler and that's how I've been modifying my Baen and Fictionwise MultiFormat stuff so that it displays the way I want it to on my Kindle.
Hope this helps.