The TCU in this car is placed in the worst possible location. The leaves you removed from the passenger side of the rain tray actually are the cause of this water, Its a bit similar to the problems that old BMW E36 sedans had, the wiper rain tray would fill with debris, water would not drain and all water would literally flood the ECU which was sitting next to it in its own chamber.

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2012 BMW X5 (Beef + Granite suspension model)

1995 E300D - The original humming machine (consumed by Flood 2017)
2000 E320 - The evolution (consumed by flood 2017)