(sorry so late but) I'm having same difficulty migrating Logic X from MacBook & Mountain Lion to iMac & Mavericks. Many aif files, old Logic songs and several exe samples did not migrate. I'm finding problems then copying by hand from old mac to new with a memory stick.
Part of the problem is I've had Logic for years. If I drop a song from Logic 7 onto the Logic X icon, it will at least open the midi info so I can reuse it. I have many such old songs which contain valuable work, but it skipped those titles (evidently the ones with old or no suffix) when transferring to the new mac.
I guess the mac thinks those songs are unusable but I don't understand why it skipped any aif files.