Automation isn't quite there yet, and with random printing flaws it will probably never will.
In
FineReader (not "ABBYY", saying "ABBYY" is like saying "are you using Mozilla?" instead of Firefox), I usually set the zoom level to fit the height of the page and go through the book using the scroll button. For each page I delete the heathers and footers (page numbers) by clicking them and tapping the Delete key. And while I'm at it, I make sure all the other recognised areas are in their proper place.
Then I save the file as .docx and set the heathers and footers from Word 2010,
exactly the same for each page. Except if it's an ePUB. Then I leave them out entirely.
Regarding styles, here's a tip:
Scan the book and use the
down arrow to go through all the paragraphs from the book. When you find a formatting style that isn't either "Heading#", "Body text" or "Footnote" you simply change it. Don't worry if you skip some of them because in Word 2010 (and possibly other text editors) you can use the Advanced Find feature
(Ctrl+F and click the magnifying glass) and find text by what style was used.
Then when you find text with an unacceptable style, you simply change it to the appropriate style and delete the "orphan" style.