I just dont want to have re re-do everything
I think what happened was that a required app for Moto Blur was deleted and that's why it wasn't showing the launcher and apps. I don't actually think all the apps were deleted. When you rebooted the phone and reset it to factory settings, it couldn't find the required app and therefore was unable to load the launcher.
It couldn't have just been just one application that was deleted; he couldn't even access the settings menu until I walked him through pushing Setttings.apk back to /system/app/.