The other day I was driving my wifes car (94 t-bird) I was raining hard and I guess I forgot I was'nt in my truck. Drove through deep water. water came over hood and killed car. I pushed the car out with a little help. electric sys seems ok. took off air cleaner and intake tube. not much water in tube. air cleaner box filled and ruined filter.  I dried car out for a few hours and finally got it to start and run ok. My question is: What else should I do to clean out this car or is it ok as is.  It seems to run as good as it did before and oil does not show any water in it.

You got lucky. Since the car has had a few days to dry out and there is no water in the oil you should be fine. You should have pulled the plugs but by now there wouldn't be any water left in the cylinders anyway. I had the same thing happen to me last year when we had all the hurricanes here in Fl (yes we had another today) yet I was not so lucky. I hydrolocked the engine. $6000 worth of damage.