This is my second post and I wanted to share an information I found lately. I wanted to remove the header and footer but couldn't manage it with Calibre since the header seemed intricate and very variable to me and tried to crop the pages with Acrobat and it seemed that it only hid the info not actually removing it. Lately I found that I can removed the hid info just like this:
"Document -> examine document
There you can delete the hidden information."
It seemed helpful to me and I'm not gonna throw the pdf files that I cannot read on Kindle anymore.
Good luck on that!