You have a $1000 cleaning kit and a free luger, JMHO.
Enjoy them both.
The long rod was likely removed from the kit in service, when the small chain type cleaning kit came into use. Later boxes were of the "small" variety and had no provision for a cleaning rod.
The small empty spot is the provision for the 9mm ejector when removed from the receiver to install the sub-caliber kit- so you don't lose the extractor!