[Moonraker]

I find the answer to this problem is not to scan the headers in in the first place. (Page numbers I like to remove manually because they aid me in proof-reading). But you don't have to scan footers containing page numbers in either.

The trick is to arrange the settings on your scanner to scan only a specific area. Do this using the Abbyy FR interface before you start. i.e. If you have a page that is 8 inches in height it is a waste of time to scan the whole A4 scanner bed. Assuming you are going to scan in portrait mode then if the 8 inch page includes say, a 1 inch header, arrange the height of the scan to be 7 inches with a 1 inch Top indent (AFR scanner settings).
If you also have a 1 inch footer then I would arrange the scanner settings in AFR thus:

Page height: 6 inches
Top indent: 1 inch

The remaining 1 inch footer containing the page numbers will not be scanned.

Once these settings are done they remain in place until you change them again. You don't have to set them for each page of the book (unless you want to).

Thereafter, you must ensure that you place the book on the scanner glass in the same position for each page scan.

Measurements for the width of a book can be set in a similar fashion.

Another helpful tip is to start background recognition in AFR before you commence. This way the scanned blocks will show exactly what is being OCR'd.