I know how you feel - I drove a car into flood water - it was dark, country lane and I didn’t know it was flooded until it was too late!

My thoughts on transmission are well documented elsewhere. Go for the manual. Like Franc says, it’s a sports car, and you throw away practicalities when you bought it. That said, the manual will give you a better connection to the car and the drive - and that’s something I really, really like about driving.