Hello Ken,
1) The CAN_NERR pin reports any static errors, flags and wake-ups to the processor (IMX53) depending on devices operating state.
2) The CAN_STBY pin is used to put the CAN transceiver into the standby mode. This mode allows to reduce the consumption of the transceiver during inactivity.
3) The CAN_EN pin is used to enable/disable the CAN transceiver.
The CAN_STBY and CAN_EN pins are definitely used by the Flexcan driver in the IMX53. These two pins are the most important of the three mentioned above.
Which version of the BSP are you using?
Hope this information helps!
Best regards.