low fuel light, and service engine, and also security light flashes

If the security light is flashing, that means the immobilizer is activated and locking you out.

Try this:

AUTO LEARN
Time required, approximately ten minutes:

1. Insure that the battery is fully charged.
2. Use the scan tool in order to clear the DTCs.
3. Turn the ignition switch from the OFF position to the CRANK position attempting to start the vehicle. The vehicle will start and then stall.
4. Leave the ignition switch in the ON position while observing the security indicator.
5. When the security indicator turns off, which can take up to 10 minutes, turn the ignition switch off. Wait 10 seconds.
6. The BCM and the PCM will learn the new code on the next start attempt.