[87esir]

I don't know why they would say the it's over when the engine is replaced that's foolish.
As for your problem it's difficult to diagnos problems like this unless it is a common problem. What kind of water damage did you have? This could be the root of the problem. I'd try the cheap or free things first like checking all your tranny sensors to make sure they are plugged in and getting good connection. If you can find out if any of the sensors can be checked with an multimeter that would also be a big help. Lastly if none of that helps I would try to find a used tranny computer cheap to swap out, and it never hurts to have things like that extra lying around.
I think its an electrical problem myself so that's the route I'd go.
good luck