Humbo337

I purchased an 03 BA XR6 project that has been sitting in a shed. When I fitted a new battery to it to try and start it, it didn't crank. Code is showing up on the stereo and the immobiliser hand is on the dash also. I cant hear the starter relay click either. Can the PCm and BEM lose connection/programming after sitting with a dead battery for a while? If so I guess a trip to the Ford dealer is the only way to get it working again? Thanks for any help.