whitearrow is right, it's so much better not to use a PDF. There are soooo many ways to grab fanfiction more easily.
For example, have you tried
Instapaper? You drag a bookmarklet entitled "read later" to your bookmark toolbar, then any time you land on a page of a story you want to read, it grabs it and saves the text. You can then download it via Calibre (through the News button) or click on the "kindle" icon on the "Unread Articles" page and it'll download to your computer. (From there you can drag it directly to your k3, or load it into calibre via the "Add Books" button.)
There are a few other really great fanfiction grabbers, though they usually only work with a couple of archives. Check each one to see if they work with the archives you favor. Also they mostly download epub only, but you can easily convert to mobi since you have calibre. Here are a few choices:
http://www.home-eisele.de/downloader_e.php Fanfiction Downloader
http://www.serdel.co.nr/ Graffer
http://fanfictionloader.appspot.com/ This one's also called Fanfiction Downloader.
http://www.halcyon-shift.net/gift-shop/squeebook/ Squeebook
Good luck & enjoy!