Security, BCM, Something??

I was having BCM problems. Reason being the middle connector on the BCM also fits a connector near the BCM, and Visa versa. We had them switched. So to let anyone know in the future, DO Not make this mistake. And yes both connectors fit eachother.

Once we figured that out we got lights, stereo, security chime, locks, windows roll up, hatch works, But the security light is the only thing that stays on now, and car will not start without jumping the theft deterrent relay (TDR) STILL.
Any Ideas?

new BCM or?

if your saying I need a new BCM, Could that be possible that it's bad and still all things that are associated with it still work?