1998 Pontiac Sunfire car went thru a deep puddle

We had a bad storm here in HI, the car was driven thru a very deep puddle. At first the car drove fine then after decending a steep hill, keeping the car started became a problem. Fuel cleaner was added to the fuel in case there was water in the lines. After that, the engine light came on. Because the car would not stay idling, the following has been replaced but car still will not idle without stalling out: boots for spark plugs, spark plugs, sensor in the dist. 7 fuel lines; oil has been drained & replaced; air filter replaced; the car has had 3 tanks of gas since to make sure the fuel cleaner went thru. I was told the head gasket was checked & it's fine, the compression is good, and the vacuum hoses are fine. The car runs better than it did, but will stall out at a stop if it is not put into neutral and the gas pedal applied. Please help with any suggestions.