I've determined the problem was bad USB ports on my thunderbolt breakout hub. For some reason ApplePi-Baker doesn't notice that something went wrong and tells the user that the operation was successful. When I do it directly from my iMac's USB port, it took around an hour and the RetroPie is booting up successfully. This will now be the second time I have to return my OWC thunderbolt interface. :( Thanks for your help!