Hello Songyuan,
If you use the 'Valve' channel on the port interface board, you don't need protection components. Those are only necessary if you are building your own valve driver circuit, to be gated by the state machine's 5V TTL output.
The state machine's port interface has I/O lines (Ethernet pins 1, 2, 3, 4) that are not 12V tolerant. Pins 1, 2 and 3 are not 5V tolerant. If you shorted 5V or 12V to those lines, you may have damaged the Teensy microcontroller.
If the damage was limited to firmware corruption, you can attempt to rescue it by pressing the white button on the Teensy board. This will put the device in bootloader mode. You'd then use LoadBpodFirmware() at the MATLAB command line to re-load the firmware. Unfortunately if the damage is physical (more likely in an over-voltage situation) it can't be rescued.
Please let me know what you find.
Thanks,
Josh