I've tuned quite a few Darkside powered Cobra's! I do a pretty good deal for my Cobra brethren.
Just post the PCM to me, and a few days later you'll have it back.
If you just want the car to run, ie. keep the standard program, I can just disable VATS (Vehicle Anti Theft System), modify the Thermo fan temps and change diff ratio settings. VATS must be disabled if you want the car to run.