o_o why are the fanfictions in PDF format?
Are they from fanfic.net or another site like that? You have two options, depending.
If it's from a one-shot, or a story with only a few chapters, just highlight all and copy and paste it into a text document, shove it through Calibre and fiddle with it as you want, and there's your fanfic.
If it's a longer story, you won't want to copy and past 50+ chapters. There are fanfic downloaders out there that will grab all the chapters automatically and make them into one document. If it's an ongoing story, you'll have to keep using the fanfic downloader each time it updates, but it's a quick, painless process that only requires the URL of the fanfic, so it's no biggie.
.... I hope this answered your question. The conversion from PDF must have messed with the document.... or maybe the document hadn't been ocr'd. Congrats on the K2!
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