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understanding pdf formatting for kindle paperwhite

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hello!

I have a Kindle PaperWhite 3 2015 Wifi (PW3).
I have k2pdfopt installed on my OS X machine. I tried it and played around options of column, justification, wrapping etc but am not super happy with the results.

I have uploaded a few of my PDFs here. They all have a common pattern to them: page numbers on the left, a large block of text that is either right or left, a small text (unit name or citation) to either right or left depending on the position of the large chunk of text and so on.

I was wondering what is the first step for me in understanding PDF internals? this is because I want to remove certain parts of text that occur in the PDFs ...for example the name of the unit occurs either to right or left and this affects the way I format the PDF should I make it all align to a single column.

Let me know if I should be clearer in describing my problem, I will draw a visual markup and ask again.

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