[Mark McLeod]

Code mostly looks okay.
Your extra motor control doesn't match your description though.
Do you see any error messages on the Driver Station Diagnostics tab?

Are your joysticks associated with the USB position that you expect? (Setup tab and click a button to see their associated USB flash on the Driver Station)

Are you using PWM cables to connect the Victors to the Digital Sidecar?
The PWM cables are hard to get seated correctly in the Victors. Try reseating the ones that continue to blink when enabled.
Check the cable orientation (Black wire to the inside of the Victor, outside of the Sidecar).

Motor 3 (PWM 5) will never do anything in your code. The case statement it's in will never be True and you call a CAN (not PWM) vi.

Autonomous Independent uses non-existent drive motors. And the DIO's are not Opened in Begin.vi (an initial Framework error, not yours).