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I have no idea about software/scanner combos; I never have any choice about scanners. (I've been working in digital imaging centers for 10 years; I get to know a lot of scanners, but they're not chosen based on how well they interface with the OCR software. Other aspects are always more important. And how well the hardware & software work together for batches of 10,000 pages is not particularly relevant for scanning a boxful of novels.)
I've worked a lot with FineReader; I'm barely aware of OmniPage. What I've heard is that FR is overall better, but that's because of features that don't matter to everyone.
FR will allow zoning templates of a sort; it'll let you create a page-zone template and apply it to as many pages as you like. It won't "ignore headers/footers," but if the pages are the same size & shape, the zoning template will do that.
FR allows customized zoning, which is important if you're working with pages with complex layouts. I have no idea how customizable OP's zoning is.
I gather that FR's OCR accuracy has increased since I've gotten it; I'm working with 7.0 and considering whether (or when) to upgrade. It does allow you to add words to its custom dictionary, so it'll learn to recognize names and obscure terms. I'd expect OmniPage to have something like that as well.
In regards to scanner choice: look at reviews at Newegg and other places. Watch out for comments like "skipped pages" and "doublefeeds." Ignore comments about pages-per-minute; they all scan slower than advertised. Find out if the scanning software allows you to set custom page sizes, because it's really annoying to scan paperback books onto letter-sized pages with lots of whitespace.
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