To be perfectly honest... you probably shouldn't convert it. Any automated conversion process will likely result in unsatisfactory results. This is because of the nature of the PDF format itself—not the conversion process. PDF is usually considered a "final destination" for a document (and it got to that destination via a one-way bridge that was burned after crossing it).
You might be better off cropping it, making sure it's properly sized for a 6" screen and just reading it in its original PDF format on the Kindle. Less headaches that way.
Other than that... using ABBYY Finereader and manually proofing the HTML results before converting to MOBI is the best method I've found. But it's often more trouble than what it's worth.
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