Don't output straight to PDF. Never, ever do that with a scanner. Scan them as images, and once you have the images, process them (I recommend Scan Tailor), then wrap them up in a PDF using Adobe Acrobat or something similar.
OCR-ing text with FineReader works just as well with JPG, PNG or TIFF. I recommend JPG (80-85% compression), since they take up less space, and the error rate isn't any different than TIFF or PNG. In fact, if the image is too clean it can have a negative impact - such as detecting smudges, dust, printing defects as commas, dots or accents. JPG will "smooth" them out a bit and the OCR is actually a bit better. I only scan as TIFF (600 dpi) the pages that contain graphics.
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