I use acrobat pro and can usually crop the header and footer easily using the crop dialog. Then I go to the document tab and choose examine document. After it searches the doc, it list the items it has found. I UNcheck metadata and bookmarks as I don't usually want those removed. I do however wish to remove hidden data, which is the header and footers I can no longer view so I leave the hidden data CHECKED. Save the pdf and import it into calibre. After that I can convert it with calibre and the headers should be gone.
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