Exporting webpages as pdfs? Losing pages?

Okay, I often open webpages on my Mac in Safari, and either export or print them to pdf to read on an e-reader, a Story HD. The pdfs look fine on my Mac in Preview, but they sometimes get cut off partway through, leaving blank pages thereafter, on the e-reader. I don't know what is causing this and what, if anything, I can do about it. I checked both the root and user libraries for internet plug-ins, but there was nothing pdf related, and there were only the system ones installed. I zoom in before exporting, so the text is more readable on the e-reader. I am using Safari 7 in Mavericks. I have the DuckDuckGo and OpenDyslexic extensions.

Okay, thanks. I tried Calibre, it can convert the pdfs to e-reader-readable epubs, but it is a pain to use, because it insists on "organizing" everything into its own folder, when they were organized into topic-specific folders, on renaming everything "Untitled," and on interfering with the e-reader when I was trying to quit Calibre and transfer over the converted versions. So if anyone knows of better options that don't insist on "organizing" and renaming everything, that would help.

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