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I was playing around with PDfmasher as well and it's fairly cool. Very easy to remove headers and footers but I was having issues getting footnotes to work.
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I've found the footnotes function to be a tad flaky with PDFMasher, but I've gotten pretty close a few time with documents that had buckets of footnotes. Close enough that I didn't mind fixing up the results by hand. And it seems to be getting better all the time. The different sorting abilities makes it pretty powerful and it's by far my favorite for very simply formatted novels, but losing italics really annoys me when converting PDF's (not PDFMasher's fault, I know).