I am finishing up my auto to 6 speed swap and need to reprogram the security system. I think. Originally I was going to just make the changes to the wiring to make the swap work. Turned out the chassis I purchased had wiring damage from mice, so I replaced the entire bulk head harness. I found two Security boxes that I transferred from the original harness to the new one.

Currently, the security light in the cluster flashes twice quickly then pauses in a repeating pattern. The key fob doesn’t work, but I can see the red light when I press the buttons. Horn doesn’t work either. Car is an 05 aero and the MT harness I swapped in is from an 05 aero.

Did I miss anything that I should swap over? I still have the original harness. If not, where can I find the procedure to reprogram the security system and key fobs?

Thanks in advance.