I cropped the headers/footers from my pdf with another tool, but Calibre still converts them
Most 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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