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Ok so in the very last pic the 2 wires that are sticking out look like factory wires not aftermarket ones. Should I be concerned or do anything with those 2 wires?
Those are the lock input and unlock input wires that go to the power door lock control unit. Normally, there is a gray 2P connector with those wire located under the dash. There probably was an aftermarket alarm previously installed and they cut off the connector. You can cut the exposed ends off and tape them up.
In the following photos, the Blu/Blk wire is most likely non-OE.
One piece was spliced into the OE Grn/Wht wire for the brake switch. Probably there was previously an aftermarket alarm/remote starter. Hooking up to the Grn/Wht wire is generally done to simulate the brake pedal being depressed to be able to start the car, by momentarily applying 12 volts to that circuit.
