BCM, or short, or something in the middle

Someone tried to break into car by prying out door handle. Pried it so far that I could get to the 2 bolts to pull the handle assembly from outside of the vehicle. We tried to bend them back, but the damage was severe enough to not allow assembly to sit flush. Pick and pull door sale weekend. So $25.00 for a whole new door seemed the easy route. Replacement was not power equipped, so we switched the insides out, and upon completion the trouble began.

First thing we noticed. Neither driver nor passenger lock buttons would lock the doors, but both would unlock all doors. I was frustrated so went home. At least her car was secure. Later I receive a message about the vehicle having different personalization options with the door locks. She doesn't inform me of the following:The car locks all the doors when she puts it in reverse. So she tries changing which mode the car was in.
Only after she does this does she fill me in. And at the same time she tells me that after trying that, the car is possessed. Chiming all the time, and locks being inconsistent. Etc.

I go pull the panel to check all the lock and handle rods, and find that the lock rod had come out of its lower position during the swap. I fix this, and put things back together. I then do extensive trial. And error tests with these results.

* When driver or passenger doors are open. Neither side will lock the doors. Driver side wont unlock. Passenger side will unlock.

* With both doors closed, passenger lock button will lock and unlock all doors. Driver side will unlock, but not lock. I then discover that if you do an even (down, down ) motion with the driver side lock button that it will lock all doors. Not too long after I discover this it seems to stop working. It also seems that it does work correctly with the doors closed at times. The vehicle acts like it is in the third mode. All doors lock when vehicle is removed from park, except it does not complete the mode because no doors unlock when the vehicle returns to park and the key is moved to the lock position.

Along with this there is a one, three, four chime pattern that repeats when vehicle is in park. It seemed to quit when vehicle is removed from park.

My first thought is we disturbed something in the door swap, that created, or exposed a short. At the same time, the passenger side seems to function fine always with the doors closed. This steers me away from anything we did. In reading different similar problems I saw someone with a similar issue get asked if the passenger side worked fine. Referencing a possible BCM issue. This persons did not, so there was no more information for me.

Does any of this give anyone enough info to point me to a probable cause, or at least to rule anything out?

If we caused a short during the swap, can I disconnect the passenger wire harness ending the short, and driver side should then work correctly?

What is up with the chimes?

Thanks in advance