Hello,
I've downloaded your configuration file and I found a few problems:
1. In the platform configuration, you need to enable the interrupts for the FlexCAN component, set a priority and add the IRQ handlers.. The lower the number, the higher the priority.

2. You need to configure the pins in the PORT components for the CAN instance you want to use, similarly to the CAN0 instance.

3. In the PINS view, you need to configure the EN and STB pins for the transceiver too, similarly to the CAN0. If the state of the EN and STB are not properly set, you might get undefined behavior.

3.1 If you want to control EN and STB at runtime, you also have to update the DIO component with the EN and STB pins, similarly to CAN0.

These are a few things I was able to find looking through your configuration file. Let me know if the suggestions help you.
Best regards,
Sorin Bancila