the car takes off when you get over 3500 rpms?
yeah thats normal for an automatic 240. The coupe we had used to do the same thing. thats why we took the interstate as often as possible. the car was just happier at the higher rpms.
as for the running better when it is cold, you might want to check you coolant temp. sensor. if it isn't working at 100%, then it could tweak things out.
The water shouldn't be too much of an issue as long as you didn't drive on it too much and the water doesn't come back. Automatic tranny fluid displaces water for that reason. Just in case a little gets in there (as in leaky radiator or something) the tranny fluid won't let the water get close enough to damage anything. Its actually worse for the water to just sit there when the car is off then it is when it is running.
as long as it wasn't there for much more than a day, you should be fine.

i know alot of people will say that you should do an intake or something for your first performance mod. However, I would suggest getting a factory service manual (aka FSM) it will help you so much.

good luck