PDF is not an eBook format. A PDF file does not contain paragraphs, lines, or even words - it's just a collection of "drawing instructions" - "draw a letter A at coordinates x,y on the page". It's generally a waste of time trying to convert a complex PDF to another format.
I would suggest that you use PDF for what it was intended to be - a representation of a printed page of a specific size - and print it.
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