The fact that he said "Driver's door can be manually locked with a key, but it does not lock the passenger door during that process. (Or unlock it)" seems to mean it's not the key fob programming. On my Crossfire, the key will manually unlock and lock both the driver side and the passenger side doors plus the trunk lock. There are some diagnostic steps given in the Service Manual that might help. In my 2005 Service Manual, I'm looking at info beginning page 8E-60.

But, yes, I agree, I wouldn't put an old alarm back into the circuit.

I would double-check the BCM connections again...but I'm just guessing.