There is no reason to think they are damaged. You can short CANBus (yellow/green wires) to 12V or ground and it won't harm the Talon SRX (or any CTRE CAN device).
For proper communication you need 120ohm at each end. Generally the roboRIO provides this at one end, and the PDP (check the jumper) at the other. Not having this MAY be the culprit.
Without 120ohm at each end, you will see some red blips IF the CAN bus is long enough. Though if the CANBus is only a couple feet and you are just playing/learning/testing you can often get away with just terminating one side with no red blips. HOWEVER you are currently in the position of troubleshooting a negative symptom that you are seeing. So the goal is to remove/rule-out each problem one at a time. So the next step is to terminate the floating green/wire pigtail with the PDP, or place a 120ohm resistor (PDP is easier), reproduce the problem, and move to the next and most likely causes (common device IDs or just wiring).
Forgetting to terminate will not damage anything.
Check the recommended gauge on the butt-connectors. I've once seen a team use a similar connector, but the connector-size was for a much thicker wire, so the crimps were not deep enough for constant connection.
You can absolutely resolve the common-IDs even with everything connected together. The is no need to separate each Talon (also explained in section 2.2 of talon srx software reference manual).
Also FYI we sell a connector strategy to make mating everything simple, and not permanent....
http://www.ctr-electronics.com/can-c...or-5-pack.html
...and other teams have found ways to connect their CAN Devices that I think are also worth looking at.
http://www.chiefdelphi.com/forums/sh...r+we idmuller
http://www.chiefdelphi.com/forums/sh...r+we idmuller
Oh hey you actually started one of the threads.