I've found PDF-to-mobi conversion an exercise in frustration and rarely even attempt it any more. Reading order is not always defined properly, headers/footers get mixed in with the main text, tables are mangled, etc.
Instead, I take a few minutes to crop margins/headers/footers before putting the PDF on my Kindle. With the cropping, I can read a lot of material in fit-to-screen view (the default), or for larger text, in landscape mode. Text can be small, but it works for me.
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