I usually export the PDF to HTML using Acrobat Pro and then depending on the results use Book Designer and then Sigil or just Sigil to create an ePub, then convert to Mobi using Calibre. Can take some time, but I'm kinda picky about how things look.
I have a couple of PDFs that, after trimming the margins, are close enough to screen size that I've read them as PDFs, but while they read fine I still prefer Mobi.
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