@chaley: Ran it against 8 books with every option checked and then one option at a time and no issues when running epubcheck against the modified epubs. Looks good. I also ran it against a total crap epub and it didn't do any damage to it (one of my wife's books that was saved to epub from a word processor -- it makes a great test for epubcheck.
)
Again, thanks very much for your time and effort!