More than likely the theft-lock sensor was damaged when you replaced the cylinder. They have a tamper pin that is easy to break off if you are not super careful and it destroys the sensor.
Was the replacement unit out of an early build 2004? If you are not sure look at the key and see if it has PK3 stamped on it. If it does that lock will not work in the 1996 anyway as it does not have the magnet to trigger the sensor in the column.
You also will need a good scan tool that can read the anti-theft data from the instrument panel. That would tell you if the issue is the key or the lock or the sensor. If you still have the original parts you could take them to a locksmith and have the cylinder repaired. May take less time and money than fighting with what you have.
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Sunday, August 26th, 2018 AT 11:10 AM