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You might try using Mobipocket Creator first to get an HTML file and look at the resulting output in a browser to see if and how things are messed up.
Some people will take that HTML, feed it into Sigil to get an epub, then to calibre for conversion after any problems are cleaned up.
The intermediate HTML code, if you are not uncomfortable reading the source, may show you that instead of black text, the PDF is calling for gray or green or some other color which does not display well.
Each line is specified at a specific place on the page in PDF, information which is not so easily processed to make sure line follows line when you convert it to an ebook format which is designed to NOT be tied down to a specific space so the text can be resized.
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