check engine light on and running rough

a couple days ago it rained alot and the local roads all flooded. so of course i had to go out driving through it. the water was only maybe 1 to 1.5 feet deep. however yesterday my check engine light cut on the the jeep seems to run a little rough when accerating through the 1,2,and 3 gears. its not as noticable in 4 and 5 gears. when i start it up and its is cold it really spits and sputters . the thing is it starts up fine and idles fine.
by the way its a 97 4.0l 5 speed
any ideas?

Live with it a few days and let it dry out, could be moisure in the distributor cap, moisure in junction boxes. Your alternator might not have taken kindly to being 'baptised' for extended periods in a submerged state either. Check your system voltage. The 97+'s take 5 complete cycles to clear a check engine code, thats cold-hot-cold for one cycle.

the check engine light cut off, however its still not running good
i will give it a few days and see what happens
thanks RichP

If the sputters continue I would check to see what CODE the ECM detected when the check engine light was lit. This will indicate what component was affected or at least get you in the ball park.
Try removing the distributor cap and look for moisture. If you find some..... blow the distributor cap out with air and reinstall.
Due to the proximity of the water; I would suspect your O2 sensor that is screwed into the catalytic converter, and next would be the O2 sensor that is screwed into the exhaust header.

problem one fixed, the o2 sensor by the cat converter had one of the wires riiped out, so i got a new one (120 bucks at stealership)
that fixed the the problem with the check engine light.

however its still running the same way it was before but its also idleing rough when its still cold. i checked the distributor cap and it was dry inside. i also unplugged all the sensors and checked them, they seemed ok no water or corrosion.
could the cps sensor shorted out? the other o2 sensor shorted out? are there any way of testing them? any other thoughs?
thanks for the help

You done well getting the O2 sensor from the dealer. That is one of the components critical it be dealership. Have seen to much variation in aftermarket versions. If someone finds that specific sensor available aftermarket somewhere, pass along that info. please. Has to be sure though.

I would guess it was the dealer that discovered that sensor was bad?? If so, this means they pulled codes?? Seeing as how your's is a '97 however, those codes should still be retrieved by the on-off method with the ign switch? Someone back me up there. Is '98 when things changed so as not to allow that technique. What was/were the codes stored? If truly running roughly, there will be codes set sooner or later. This indeed will point you in a direction. So many things affected by high water could be the cause.

Judd,

You are correct !!!! 1998 was the first year that you can no longer retrieve the codes with the ON/OFF/ON method.
I am sure you are correct that the ECM will throw another group of codes for the rough idle. Could be the CPS or the other O2 sensor.

how does the on/off method work?

the check engine light is also back on, and its getting about 4 miles less to the gallon than it was before