Grand Am drive into flood

I have a 99 Pontiac Grand Am with a 3.4l and auto trans with 70,000 miles. At work, I had to drive it through a flooded road. Apparently it was deep enough to suck the water into the engine and stall the engine. The water level was up to the doors. I had to pull the plugs and drain water out of the drain pan and crank the engine to remove the water from the cylinders. The engine did seem to spin quite freely so I assume everything is ok internally.
My engine light did come on after taking it to the closest oil change center on the way home from work after getting the engine to start again. I didn’t have a scan tool handy but since it appeared the trans was slipping I took it to the local trans shop. They pulled a code 121 for the TPS. The TPS was registering at either 10 or 20 percent angle at closed throttle. I cannot remember if he had the engine running while checking it.
I am having a hard time believing it messed up the TFP from flooding the engine. I would be more inclined to believe I had messed up the IAC or MAF sensor. But the code indicated the TPS. It did of course cause the trans to shift hard and want to jump right to second gear after about 40 mph and with slight peddle movement.
Is it possible that dirty water could have caused the IAC to not move freely or something in the water to cause some blockage or keeping it open and still give me TPS codes with no other codes? Or even the MAF sensor being damaged from the water?
I did borrow a scan tool from the local auto store and got a code 121 and 122. One deals with the range and the other low input.
The idle is either low at 650 or high at maybe 1100 or 1200, sometimes about 1300.
When I unplug the TPS the idle goes to about 850-900.
Also the trans place recommended to have them service my trans. They wanted to pull the pan and put it on the machine to change the remaining fluid. I worry though that they will just stick ATF 3 in the trans and not properly check the level as it does not have a dipstick and requires a special trans fluid if I recall correctly. Will water in the fluid allow me to visually see if its contaminated? I am having a hard time recalling some of my trans knowledge from school as I never really got into auto trans repair afterwards.
Also anything I should also know that I may have forgotten to check or take care of aside from removing the water from the crank case and cylinders, oil change, and air filter?
Thank you for your help,
Mario