Welcome to the forum! To program your new fob, simply follow these instructions.
Entry Remote Keyless Entry (RKE) transmitters to your vehicle. To match an RKE transmitter to your vehicle:
1. Make sure the vehicle is in PARK (P).
2. Press the vehicle information button until LEARN REMOTE KEY PRESS V TO BEGIN displays.
3. Press the set/reset button until REMOTE KEY LEARNING ACTIVE is displayed.
4. Press and hold the lock and unlock buttons on the first transmitter at the same time for about 15 seconds. A chime will sound indicating that the transmitter is matched.
5. To match additional transmitters at this time, repeat Step 3. Each vehicle can have a maximum of four transmitters matched to it.
6. To exit the programming mode, you must
cycle the key to LOCK/OFF.
I would be happy to, however I cannot access the file you linked to. The link appears to be broken and I cannot find the TSB you are referring to in my resources. I'm not showing any brake light issues on the 2006 Malibu. Do you know the TSB number off hand? I look forward to your response.