I have a '99 Chevy Blazer 4.3 V6 automatic. We had a flash flood hit us earlier this week and I hit a puddle that was a little to deep. To make a long story short, I have changed out the oil, oil filter, transmission fluid, transmission fluid filter and the rear-end oil and the blazer is running again. The problem is the transmission is shifting into 2nd and 3rd gears at higher then normal RPMs. Other than that everything seems okay. Dose anyone have any sugestions???

yes, remove the negative battery cable from the battery for 10 minutes to reset the computer.

See if it will help.

I tried disconnecting the battery. This made the SES light go off, but it is still shifting the same way.

How far did the water come up?

The water came up to just below the bottom of the doors, but when I went through it I think that a wave of water went over the engine. I know that it sucked a lot of water up throught the air intake. There was water on top of the pistons and a lot of water in the oil. I changed out the spark plugs and flushed the water out of there and changed the oil and oil filter which got the motor going again, but the transmission is still acting up. Could the Throttle Position Sensor have anything to do with it?

Throttle position sensor could affect it, so could the vehicle speed sensor, is the speedometer accurate? Could try a new fuel filter

The speedometer is accurate. It gets up to about 20mph before it shifts into 2nd. Can the fuel filter effect the way the transmission shifts?

The water came up to just below the bottom of the doors, but when I went through it I think that a wave of water went over the engine. I know that it sucked a lot of water up throught the air intake. There was water on top of the pistons and a lot of water in the oil. I changed out the spark plugs and flushed the water out of there and changed the oil and oil filter which got the motor going again, but the transmission is still acting up. Could the Throttle Position Sensor have anything to do with it?

I would change the tranny fluid again and swap in a new VSS (Vehicle Speed Sensor) on the tranny.

Also, change the oil again seeing it is almost definite that you didn't get all the water out the first time.

Trust me on this.

If the fuel filter is restricting fuel delivery, you usually have to give it more throttle to keep speed and since the PCM uses the throttle position and vehicle speed to determine shift points, it affects tranny shifts

I replaced the Throttle Position Sensor and that fixed the problem. It is shifting perfectly now. Thanks for all of your help.