If you are scanning the files and OCRing them yourself, whatever format you have made your corrections in would probably be best.
I use epub because I use calibre and epub is the base for many of its functions like search and replace etc. And the calibre viewer also converts non epub files to epub for display.
I am not touting epub superiority, because frankly most formats seem fine to me, but epub also seems as good as any other formats to me.
Helen
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