I had trouble converting large pdfs with Kindle.
There are probably lots of tools that work but the one that seems to do best for me is Mobipocket Reader for the PC. This will convert PDFs to Mobipocket files (of course). From there the Kindle conversion tools will probably do a pretty good job.
You may have some trouble finding out where Mobipocket reader puts its converted files--you need to look at the advanced settings to see what directory it is using.
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