I have to toggle this on Rung 9 to make it go off on Rung 0.
No, the Run/Stop Input I:0/1 is used on both Rung 0 and Rung 9. Inputs can be used in many places, and all duplicates operate at essentially the same time. On Rung 0, when I:0/1 goes ON, it serves to turn on the System Run Relay B3:0/0. On Rung 9, when I:0/1 goes OFF (when the system is OFF), it resets Counter C5:0.
I:1/0 is your maintained-contact Run/Stop selector switch, and is an Input to the PLC. The PLC has absolutely no control over Input devices. It cannot turn them either ON or OFF. The PLC only has control over its OUTPUTS, the actionable devices.
Normally, a Run/Stop selector switch is designed to be operated by nothing other than a good ol' human hand.
If you want to improve the program slightly, then use 2 control inputs for a traditional "3-wire control circuit", with a normally-closed momentary-contact Stop Pushbutton and a normally-open momentary-contact Start Pushbutton, with a seal-in contact from the System Run relay in parallel with the Start Pushbutton. Then when your program reaches its end, it can turn off the System Run relay, and can only be turned back ON by pressing the Start pushbutton.
The advantage of using momentary-contact pushbuttons is that the system will not come back on after a power outage. Using a maintained-contact selector switch can cause a system to restart in RUN mode when no on is there, or when someone is there and in a dangerous spot.