I use Acrobat 9 Extended, you can go to crop -> box crop, works good for cropping out borders also, like how they put ISBN info and page header/footers. That way you get just the document body.
Then you can use acrobat to renumber the pages (i-xi for the preface-> contents, and then 1-500 for the body), so that the contents of the book aligns with the PDF page numbers in the PDF viewer.
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