Looks like victor has taken care of the one question. More than likely, you've got a faulty oxygen sensor. That's what the CE problem usually is, but, run the codes to make sure.
As for the security system, sometimes when the battery has been disconnected for a long period of time, it will lose programming. Get in the car, turn the security system off (no blinking in security switch) and turn the ignition on (don't start the car, just turn the switch to the "on" position, and then, off). Immediately begin to push the security rapidly until you hear a couple of quick blips from the horn and a clicking coming from the glove box. Press the button on one remote twice (the horn will sound with each press to confirm receipt of the codes), then, press the button on the second remote three times (again, the horn will beep to confirm signal receipt), then, turn the ignition switch to the on position and off again to remove the system from "program" mode. Pretty simple, huh?