Viper 4x04

So here is what i have. A buddy from work asked me if i could program another remote for his viper alarm system in his 06 Lincoln Navigator. I said lets guy the same remote you already have and i can program it. Get the remote (LE model, black with lights on the side) and go to program it and the system wont let me in pairing mode. Tap the button on receiver on the windshield once then once again and hold it. I get no chirps, no led light, nothing. Try it a few times as the instructions tell me too. The door is open. Now, i look under the dash and see its a replacement brain. The number on it reads 4x04. So i'm assuming it replaced a 4204 but i'm guessing. He hasnt found the book for the original yet so i'm not sure what im working with here. His current remote does everything it should but i cant get the new one to pair up. So i'm afraid that a door wire or some sort of trigger isnt wired up for me to enter pairing mode. I dont think the hood switch was ever wired in. So my question is, should i try to unplug the unit and see if it will pair after a reboot? I do have a bitwriter but wasnt sure if i could use it manually program a spare remote off of the bitwriter or not? I read around a few places and some people said they had problems and they unplugged their units and then their org remote wouldnt work either so i'm afraid to do that and him be out of a remote completely. Any suggestions would be great. Thanks