Dumped wifes jeep in mud hole

a few weeks ago I was driving down some logging roads and I accidently drove my wifes jeep into a mud hole that had, oh.... atleast 3 to 4 feet of water in it. I thought that I had turned the engine off before the air in take box when under. I got a buddy to pull me out about 15mins. later.
About an hour after we got the jeep out I started the jeep and it fired right up but now about two weeks later it wont start with the exception of twice and both times it run rough and had water coming out of the exhaust pipe. Anyone out there that my have a ideas as to what is wrong I would be very greatful. It an '89 cherokee larodo 4.0L in-line 6

Was it run between the first time after the dunking and the two weeks later?

If not, you may have cracked something submerging a hot engine in cool liquid. Check the oil and see if it looks milky

Was it run between the first time after the dunking and the two weeks later?

If not, you may have cracked something submerging a hot engine in cool liquid. Check the oil and see if it looks milky

It was started about 45mins after it was dunked and not again until two weeks later. I also did checked the oil and it seems to be fine, and when I got it to fire up the oil pressure was pretty good. It was just running real rough. Almost seemed like it may be some kind of fuel problem but not sure where to start looking and I can't explain the water coming out of the exhaust. This may be of no importance but the exhaust itself has a fuel smell to it like its running rich. thanks very much for the help. And any other advice you may have.

I would check you CPS especially the connectors.

I agree with MrBill. Check all connectors. Clean them out with alcohol and put a little dielectric grease in. Also check that your tank didn't get water in it. I'll bet the exhaust water was sucked into the muffler.

thanks for the advise I will give that a shot and see what comes of it. Once again much appreciated

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I can't explain the water coming out of the exhaust
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If it's just a little water right at first? No big thing. Water condense in a muffler as she cools.
If it keeps coming? Bad new. Good chance you lost a head or head gasket.

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It was just running real rough.
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Could be a lot of things including bad H gasket.

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This may be of no importance but the exhaust itself has a fuel smell to it like its running rich.
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It is common for a rough running engine exhaust to smell. She not hitting on all six for some reason. So it maybe no big deal to.
After Cleaning and drying and sealing. Check the air filter and box. The tube ribs can hold some water to. Clean, dry, and replace as needed retest. If no help.
Pull plugs and watch for wet, rusty, or even green plugs. If you find one run compression check. If compression is OK replace plugs and test run engine again. If compression test bad then you will need to pull the head and repair or replace as needed. LUCK

thanks a very much badron
I will look in to that.

Happy to report that I think I got her fixed I found no problems with the compression and all cylinders are dry. I did drain my tank and then put 5gal. preimum in her along with some gas dry,fuel system cleaner, injector cleaner and some octane booster(a little over kill I know)and she fired up and has been running strong for the last two days! Oh I also replaced fuel filter and replaced some shabby looking fuel line while I was underneth her but I hope(crossing all my fingers) that I got it fixed! So thanks to everyone for the help!