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I use pdftoepub by DNAML. It is good for removing headers, footers. Result looks nice. Easy to use, there are some optional steps for advanced users. It's free now.
The only downside would be that you need to convert individual files.
I used finereader a lot for school work. It's a great program if you need to have text from pictures/scans. But it does make a lot of mistakes. Maybe with English language it works better, less complicated characters.
Will have to check it out again.
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