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The way I would create eBooks is to first create the ePub and get it looking just how I want it. After it's been looked at and proofed and is ready to go, convert that to Mobipocket. You won't have to worry about typos or whatnot creeping in as all that's already been proofed. The next step would be to see how it looks and if it looks good, then that's done.
One problem we have with publishers can be worse then OCR. They sometimes use a PDF source.
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