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1) If you know the guy doing the scanning, why not get him to send you something a little more basic than a Word file? Surely he has an interim format that is more useful to you.
2) Any chance you could post some fragment of a file here that we could take a look at and try with various ideas?
cap
ps: I once reformatted a scanned PDF to HTML conversion that took something like 60 hours of work to make look right. I'm still not sure it's completely correct. I certainly won't do it again.
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