Hmmm, I'm not sure what could get damaged that would stop 2 of 6 cylinders from firing.
Your positive you wired the camshaft position sensor correctly according to the diagram?
Did you check to see if any other wires were hit by the belt, like the ones going to the crankshaft position sensor?
If all of that checks out I am not sure what could be causing that coil pack not to be commanded to fire.
Hopefully somebody else has some ideas, I'll try to do some research, and see what I can dig up, but I've not heard of any others having this problem after replacing a connector for a CMP, or CKP.
It is definitely not your ICM, coil packs, or plug wires, as you have ruled those out already.
You may end up needing to verify all the wires coming from the ICM, going to the CMP have no more breaks in them, can you use the diagrams, and a multimeter set to ohms to verify each wire does not have a break, from wire end to end you should see 0 ohms of resistance.
2006 Pontiac Grand Prix GT with SC
1996 Buick Park Ave NA