I don't have much to add, but want to follow this thread since I have a Canon DR-2050C. Great scanner and I love the duplex scanning feature.
What I can tell you is, if at all possible scan to html instead of pdf. At least that's what I gather from skimming the various sub forums here, especially the Calibre, ePub, and Workshop forums. ABBYY Finereader is fantastic software.
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