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There is no one magic fix that resolves all issues with all PDFs. In fact, most "fixes" only work on a particular narrow range of PDFs. You'll likely have to try a number of tricks.
One such trick that has worked for me is to open the "evil" PDF on a PC using Adobe Reader and then printing it to disk using a PDF virtual printer. These virtual printers are system level print drivers that write out a PDF to disk instead of feeding data to a hardware printer. I've used PrimoPDF and BullZipPDF successfully.
The resulting PDF looks just like the original but is "flattened" of any and all elaborate features (layers, transparency, ...) making them easier to render. I've found that most PDFs downloaded from Archive.org fail to render properly on my Kindle Keyboard but when I use the trick above the new version displays properly.
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