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It's your choice of PDF as a starting format that's the fundamental problem. A PDF file isn't a "book" - it doesn't contain paragraphs, sentences, or even words, as any normal text document does; it's purely drawing instructions of the form "draw this shape at these coordinates".
For future reference, you'll probably get much better results if you start with a good OCR program (Abbey FineReader works great) rather than with PDF.
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