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If you find it let me know.
When I'm truly desperate I use Nitro PDF editor and use the page crop function to take out headers and footers (page numbers etc). I then export it to a DOC file then open it up in Word and save it as a html file. Then I put that in Calibre and convert it to mobi.
And even with ALL those steps I often get a crappy Mobi file and I suspect that your file has a bunch of tables and graphs and images given the problems you are having.
I'm sorry to say that my short answer is that the Kindle still doesn't handle PDF files well and I usually have to read those on the iPAD.
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