I suspect the "formatGood" books you've seen were topaz (as that's the only one to use any font other the built-in ones). The only way to create those is to print the PDF and have Amazon convert it (costs about $195, from what I've gathered).
Otherwise, try something like an PDF to Word or HTML converter (mobipocket does a decent job of html, but can't deal with tables); from Word, convert to HTML and then edit in a good HTML editor to fix your tables and such (but you'll still only get default fonts, so don't bother setting them in the HTML), the convert to mobi.
Or, just put the PDF on the Kindle and view it sideways - on the DX, this is almost 100% size and works pretty well.
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