How to backup Android system and Apps with their configurations?
So from what I understand, you managed to back up and restore the ROM itself (system partition) but not the apps. Basically I'd recommend:


Backing up the ROM with the backup option on recovery. I don't remember if it means your apps will be backed up as well but I think it does.
You can use Titanium backup or Hellium to back up your apps. The backups will be saved on your phone so after your backup, transfer the backup files from your phone to your computer and once you're done restoring, transfer those same files from your computer to your phone and use one of these apps (whichever you chose) to restore your apps.
Notice that you can backup system apps as well but it is not recommended as it might give you FC's (force close).