So after many hours of in head troubleshooting and reviewing of information I came up with a theory as to why the remote start was not working. It worked when we had the doors open and closed. But not locked. you see the Alarm double locks the car. Which kills the ingition switch/starter. So the remote start works if the doors are not double locked. So now I have a proceedure to have it work unlock, start, relock, wait until time to go, unlock, get in and go.

I'm not sure if this is a) a design flaw in the alarm b) something that a previous owner has done to my car causing the problem c) something we missed, which i doubt at this point, d) tapped a wrong cable for starting e) all of the above.