When the key was obtained, did you get the key with the correct resistance as the old key?
There are 15 different resistance ranges.
What exactly do you mean the key was fixed by a locksmith?
Do you mean they had to determine the cuts that needed to be made to the teeth?
I would go ahead and get the VATS bypass module Justin linked you to, and have it installed, then if the car still won't start, at least you will know for sure the VATS system has nothing to do with it.
I don't think the running rough, and dying issues you mentioned, are from your VATS issue, once the car is running VATS won't cause it to run rough, or die.
Have you ever gotten any DTC trouble codes?
2006 Pontiac Grand Prix GT with SC
1996 Buick Park Ave NA