Supercharger installed, CAR WON"T START. HELP PLEASE

What's up guys. I had my friend who is a prof. mechanic install the Vortech V2-SQ today. It took about 7 hours for him to install. Everything is on the car now, but we have run into some problems. At first the car wasn't running correctly. They told me that half the engine was running extremely rich, and the other was running fine. After a few attempts at analyzing the problem, they realized that one of the injectors were blue in color, and the other green. So they think that I have an incorrect set of injectors. The second problem that they ran into was the car won't start now. The anti-theft light comes on everytime they try to turn the car over. Is there anyway to correct what is going wrong with my car? Any help would be very helpful to us. Thanks.

So the car won't start with the Superchips chip that came with the car, but if we take the chip out the car starts. The Chip turns on the Anti theft light which is the reason why the car won't start. Is there a difference in the computers from 2001-2002. The kit came off of a 2002 GT. What are my options from here. What does PATS mean?