It will require a bit of work:
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There are page numbers, headers, or footers in my outputYou need to use Calibre's Search and Replace feature when converting from pdf in order to remove any text you don't want. These require the use of a search syntax called regular expressions. If you are intimidated by regular expressions, many Windows users have reported that Mobipocket creator is a good alternative to use to do the initial pdf conversion. Use Mobipocket Creator to convert the pdf to the .mobi format, and then use Calibre to convert from mobi to your final desired format.
I cropped the headers/footers from my pdf with another tool, but Calibre still converts themMost pdf cropping utilities only change the visible page boundaries of the pdf, they don't actually eliminate the text data.
You need to find a utility which both crops AND deletes hidden text. Very few tools do this - Adobe Acrobat has an option to 'remove hidden text' while optimizing pdfs which can facilitate this. The alternative is to use Calibre's search and replace function to delete the headers, or use Sigil after conversion to epub.
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