My guess is you still have issues related to the immobilizer getting wet. The fact that both of your windows drop on opening is a good thing. The chances of both of your windows not working at the same time are remote at best. Then add in your key fob not working at the same time.
If you have a multi-meter and experience, you need to start tracing circuits. There is a plug from the door to the A-pillar. My driver side plug got water in it and caused several issues/problems. Mostly window issues. The locks, window, lights and sound run through that plug. Check and see if it is dry.
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