I, too, am a big fan of ABBYY Fine Reader. There is a selection to remove header and/or footer, and there is a bulk page trim feature.
As ABBYY scans your document, it selects image or text regions. Sometimes there is an error, but it is very easy to scroll through the pages and change the type of read area, then re-read just that area.
I like to save to html, make little repairs using Word (or make a hyperlinked table of contents, which is very easy to do in Word), then let Calibre to the conversion to mobi.
The last book I scanned, the only things to fix were line breaks and pictures that had text in them.