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Using BRISS to convert to single column could be a useful step. I suggest that format you use for storage and to rework the data should be ePUB. Sigil is a good ePUB editor and you can capture images, metadata, text all in one ePUB file making the management easier. HTML is easy to convert into ePUB so it is a good choice for the initial conversion from PDF but any text form that supports formatting would also be ok to get to ePUB.
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