Thank you for the responses.
I wasn't aware ISBNs on ebooks was different, or that some don't have ISBNs. I don't care about the particular version of the books. My goal is to find an efficient way to get mainly the title, author name, and cover for my iBooks before converting them.
@davidfor - In my primary Books folder Apple has a .plist that contains information on all the books I've downloaded. It does have the information I need, but also a ton more, and is probably not in a format a program can parse out the information I need.
I think you are right, that I need to go through manually and add the titles and authors. Hopefully then I can pull covers automatically (although covers aren't a HUGE deal to me). Guess I know what I'll be doing during conference calls for the next couple weeks.
I do wish there was an easy way to tell which books have DRM so I can just delete those from the library before doing this. Oh well.