If you use Finereader's "save to Word" option, you'll find a "remove headers and footers" option cleverly concealed in the Word save options. It's a lot easier than cropping.
Joining up consecutive pages is best done manually in my personal opinion. You may sometimes need to check the original to see whether a new paragraph begins on the new page or not, or whether there is a scene break. Removing the page dividers then becomes part of the process of skimming through the Word file to clean up gross formatting errors.
Another advantage of using Word is that its spellchecker is easier to use than Abbyy's, and it has excellent search and replace capabilities that you can use to fix common errors quickly.
By saving the corrected file to filtered HTML, you get a file that Calibre can convert to various formats.
That said, everyone has their own workflow (and mine is in a state of flux at the moment since I've switched to reading .epub).
