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I guess my first question is do you have to use the PDF as your source file? Does he not have the original Word (or whatever it was written in) doc for a starting point? PDF is one of the worst source formats you can begin with.
If I was formatting this and my only choice was to use the PDF I'd use Acrobat or some other tool to export the PDF to HTML and use that as a base to edit and build an ePub using either Sigil or the Calibre Editor. Auto converters are generally not going to cut it. Once I had the ePub how I wanted it I'd have a good source format to either upload to stores as is or convert for the Kindle store using KindleGen/Kindle Previewer.
The easiest way to avoid those page numbers and headers is to crop them out of the PDF before doing anything else with it. Just be sure it's really cropped as some programs will just hide the cropped area and those things will still show up in a conversion.
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