Aperture library won't sync through iPhoto to an iPad
There are many facets to your question and I will try to answer all of them.


If the error you are getting is an iTunes library issue, then you should reboot itunes holding down the option key, and browse to the existing library file in /Users/username/Music/iTunes/ this reloads your proper library.
iPhoto can open your aperture library, however it's usage of RAW files etc, it limited.   this link has some more info about using Aperture library in iPhoto. http://support.apple.com/kb/HT5260
As the file extension on the library should be .aplibrary you will need to choose aperture from the drop down under Photos in iTunes.  iPhoto is only acting as a viewer for this library, and is not "holding" these files.  
You should be able to choose "import to library..." in iPhoto and choose the .aplibrary file and it will import these photos into an iPhoto library.  However, in case you decide to begin using Aperture again, save the aplibrary file. Note:  you may lose some, if not most of the edits made in Aperture. 


Question:  Why would you want to revert back to iPhoto?  If you have a coveted aperture license, why not use it?  On the Retina MBP this program works even better, and looks amazing.