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The best solution is to convert the PDF into ePub, edit the ePub so it is how you want it t o be and then convert to Mobipocket for your Kindle. the reason for doing it this way is that ePub can be edited where the Mobipocket cannot so easily. Plus, ePub to Mobipocket usually works well.
Now the conversion from PDF is going to be a problem as it cannot be done without errors and the only way to fix the errors is to A/B compare the PDF to the output.
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