2002 Chevrolet Cavalier Shifter stuck along with key

My gf lost her key so she had a new one cut for her cavalier that's when all the problems started. One day she started the car but the vehicle would not come out of park we unplugged the battery which did nothing. So I pulled the fuse to the fuel injection and the vehicle shut off. I took off the steering cover and released the ignition switch to get the key unstuck. But when I hooked everything back up. The car again started but wouldn't come out of park and the key wouldn't shift back so I had to repeat the process I stated above. I think it's the security system because the light flashes but the car starts and doesn't shut off. So I feel like I'm running in circles.