This is a pic of my CPU, my question is do I have a chip? I've been told that if it was stock it would just have a rubber plug in it

 

No you don't have a chip , but if you do it's in your J3 port

 

Hmm there should be a black rubber plug on the opposite end from the wiring harness. Perhaps the cobra ECU has a different cap. I've had two diff SCT chips, one had a black metal top that went over the side and screwed down to the ECU on the side, my current is a SCT 4bank with no cover(chip) is visible. That looks like a cap.