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Good idea unplugging the amps. I'm betting they were connected incorrectly and were always on.
Gotta watch the aftermarket stuff. I had a local audio shop put a driver side seat heater in a 2005 Lincoln LS. They tapped a circuit in the fuse box that was always hot. So I had to double check every time I exited the car to make sure that the switch was turned off.
Both batteries need replaced at the same time. I'm now guessing you don't have a parasitic draw. You just old batteries that needed replaced. When one dies, it will start to kill the other one. That is why the passenger side is now dead.
So now you need to replace with 2 new batteries. Otherwise you will have this same scenario happen again. That's one expensive lesson.
What you say is accurate, but try to get a Ford dealer to replace both batteries when they say one is bad....