My wife's 04 cooper was flooded in Hurricane Harvey. The water never got into the engine but did get inside up to the cup holders. I don't have the option of replacing the car so I've been working on it to make it work again. I've pulled the interior and cleaned every electrical connector and the fuse block. The car is running and everything seems to be working again but when I'm driving it the transmission will do strange things. Sometime it will not shift, while other times it will constantly upshift and then downshift and then there are times while at a stop light I have to hold the brake hard as it seems like it wants to move forward and bogs the engine down. I've changed the fluid and the old fluid didn't seem to look bad or have water in it. Is there a module somewhere that controls the transmission that I need to be looking at? If so where is it located?

 

Would think "up to the cupholders" would be close to the bottom of the trannie/engine. have you removed and cleaned all the plug connections going into the transmission? Would also think the BCM over in the passenger foot well is toast (soggy toast).

Hopefully some others will chime in. Good luck.

 

Did you ever solve this? My daughters CVT transmission started doing similar things after she hit a GIANT puddle during hurricane Mark.

Regards,
Peter