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You are asking more then one question.
First, to the “what’s the best one”:
The market leaders are Omnipage pro (now in the 16th version) and Finereader pro (now in the 9th version).
Both are outstanding and both have the possibility to take out headers and footers (inclusive page numbers), but… and there is always a but, it as to do with the format you save your OCR’ed file.
One possibility is saving in text format, even so, it’s not 100% accurate.
I have got situations on getting more then 95% of them out with some projects.
If you have the money, go with one of these 2, you will not regret it, and with the OpticBook you have the perfect twin machine to convert books.
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