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As noted by Toxaris, just plain slogging. There are very meticulous epub creators here that go through their submissions to the library repeatedly correcting previously unfound errors.
Your post also does not mention the significant problem of what flavor of epub, for which machine. Hitch makes her living weaving and dodging like a Superbowl quarterback among the creative variations the actual device manufacturers have put into their machines.
Lastly some things, like tables, pull quotes, etc will work only so long as the user stays within a certain size range. So a technically correct epub may not be so hot once you try to use it in a particular device.
Distributed Proofreaders, the group that checks Project Gutenberg books, has some software they use which allows viewing a PDF and another document together for proofreading. But I don't know if it is available or adaptable to your purpose.
I wish you much luck. You are going to need it.
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