I"m thinking the trunk lid is not indicating that it is closed. Im just not sure where that wire is.

I BELIEVE all of the following is the way it works:
The "trunk lid open/closed" indication goes to the Body Control Module - to turn the dome / trunk lights on and off.
That output (to the lights) has I timer in it, the timer is in the BCM.
The BCM then goes onto the CAN bus and tells the Top Control Module the status of the trunk.

Have you downloaded the manual? It is time to! I did so a LONG time ago and I THINK this is what I'm using:
http://www.jodykrivohlavek.com/_docu...ice_Manual.pdf