For future reference, a free OS X app
AppCleaner will remove all of an app's supporting files when you want to completely uninstall an app. As you've discovered, calibre has supporting files that also need to be removed when uninstalling.
Also, from the debug trace you've posted, it looks like the Goodreads Covers plugin fails during initialization, and you have more than one iDevice connected, which the iOS reader applications plugin is complaining about. But, on the bright side, you're up and running again.
G