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pdfReflow + calibre = good job!
pdfReflow does a great job removing headers. Even though the result might not be too pleasing to the eye (I opened the resulting html in OpenOffice and didn't like what I saw: quite a few different font sizes, lots of space between paragraphs, etc), Calibre produced a quite decent document. This is cool stuff, hanks!
By the way, I used the GUI, haven't tried the command line.
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