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Welcome to MobileRead, dyvaris.
Although calibre does a good job with many PDF documents there are times when the very natrue of a PDF can frustrate calibre's best attempts. I use PDFs in native format with my Sony reader and I believe that Kindles also have good support for PDF built in.
You can add PDFs to calibre and manage their metadata without converting them to another format and use calibre to send them to a reader.
If you still want to convert your friend's book then maybe you could get a copy in a more suitable format, such as html, since your friend presumbly still has the source for the book.
With regard to page numbers, I would simply let the reader handle this itself rather than trying to code it into the document.
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