Factory Anti-Theft System activated, how do I get the lights to stop flashing while driving?

It has a recall on my key ignition and got it replaced and had replaced the vehicles battery I still couldn't get vehicle to turn over. It ran for a couple seconds then turned off. Then it wouldn't start again. I have now replaced and reprogrammed everything from the PCM, Immobilizer, another key ignition and key fob to finally get the vehicle to start and run. But now I cannot get my factory anti-theft alarm to shut off. I have pulled the fuse for the horn so you cannot hear it right now. But when I get in vehicle and start it up and drive down the road, my outside headlights, and all exterior security lights flash for the whole trip. When I park and shut the vehicle off and get out of the vehicle the security alarm will go for about maybe 3 minutes then shut off. How do I get my lights to stop flashing while I drive? Help