I don't know about the software your using, but I use acrobat pro and usually I crop the header and footer first. 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. After that I can convert it with Calibre. The software your using should offer a way to remove the hidden data once you have cropped your document. I hope this helps
