According to the tech working on the car, 1st and 2nd gear were out of tolerance requiring a full rebuild of those gears. It was an issue from the day I picked it up where it would intermittently pop out of first while driving slow like through a parking lot.
I was surprised when they said it had flooded, the dealer stated sometimes the injectors will leak or not close and cause a flooded scenario. This was new to me. It has happened a total of 2 times.
The rattles I knew to expect before I bought the car. I do get small rattles and vibrations in the interior panels and trim but the rear seats are full on clunking, almost like a strut clunk. I know it's the seat because I can lay them down and it stops.