Not sure how to attached files to posts, but I can e-mail you the pin-out assignments for the 94/95 GT. For the grounds I doubt the Cobra is different. Hope this helps. It is a good idea IMHO to jump the 20, 40 and 60 pins to the negative battery terminal by running a dedicated wire.
Checking the grounds is a good exercise in any case, but I'd think about other influences as well. Was there any mod done or symptom seen just before you had this problem?