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The problem may be your OCR software. I bought ABBYY Fineware for about $100 and scanned a novel into Word 2000 in fairly large gulps, say 10-20 pages at a time. To the best of my recollection, Fineware simply ignored the headers, page numbers, etc.
The biggest problem I had was the combination UM in lowercase. I can't remember how Fineware translated it, but it had nothing to do with UM. Since the novel was about ski-bums, I finally had to do a search & replace to fix them all.
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