Once the floor is dried out, plug the holes. Sounds like you got water in because a plug was missing and it moved to the rear of the carpet. Remember, the foam padding will absorb a LOT of water.
9 inches of rain? That creats a lot of puddling on the right side of the road which should then splash up more on the passenger side.
Water should never get into the car, it can do considerable damage if left there. I doubt that the sunroof drains are clogged, but it is easy enough to check: pour 1/2 cup of water into each drain hole, the water should immediately pour out beneath the car.
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