I have a similular senerio as you...my engine was submerged in water but I have a snorkel on the intake so I never hydrolocked it. But I have been researching the problem for a bit and it seems that it has to so with "heat soak" which means when the engine gets to normal operational tempatures than shut off for about 10-15 mins exhaust flows back into the #3 cylinder and causes it to misfire. I have a check engine light on now I'm going to pull the code to make sure this is the problem, if I get it fixed I'll be sure to let you know!
96 Jeep Cherokee 4x4 high output 4.0 L6 automatic
Let me first start off by saying I recently took a swim with my Jeep accidentally while trying to pull a friends Ranger out of the local swimming hole. Mainly the front end was submergerd with the rear slightly out of the water. The water came the bottom of the steeing wheel. I knew that I was in trouble when the water ran across my lap.
After towing it out of the creek, I drained the oil/pulled the plugs and blew out the water out/used a turkey baster to suck the water out of the throttle body/dried out the distributor/replaced plugs,oil filter,air filter/changed oil several times. To my surprise after doing all this, the jeep started right up and ran fine... that was, untill it got warm...
It runs/idles just fine cold, but as soon as it warms up my idle goes up and down rapidly. It does not seem hinder it while driving on the highway, however when I come to a stop, the idle is going up and down and sometimes it stalls. If I start it right back up, it idles fine for a minute or so, then goes right back into the jumping idle.
I took it to a local shop and he put a diag tool on it and he said I'm running at half vacume and the throttle position sensor reads 0% when in idle. I'm not sure what he ment by half vacume, and we were not able to find a vacume leak anywhere.
I have had some friends tell me its the PCM, and others say its oxygen sensor, crank position sensor, water in the gas etc... I have yet to get a straight answer, and I know it's a problem that could be caused by several different things. So it's hard to tell. I have read about people chasing this kind of grmlin for months, and spending a ton of money doing it, but this more or less a weekend driver/farm Jeep that I really don't want to sink a bunch of money into.
My question is, has anyone else experienced this problem after submerging their Jeep? and if so, what was the cure?
It's a great running Jeep, and I love it to death. It still pulls like a mule and all the power is still there, it just does not want to idle properly, and the stop light stalls are getting more frequent.