Darn it BTLT, it's kina hard to help if we don't know what you have for a rig. Carb and EFI makes a big difference here on how we'd answer the question. Let me cover a few things that ain't been hit yet.
If the engine has asperated water and you pull the plugs and drain the oil, don't refill with oil prior to cranking the engine. Fill that puppy up with Diesel Oil. Yep, good ol' truckin' crude! Then MANUALLY rotate the engine as you start pouring Diesel into the open cylinders (Ya know, where you removed the spark plugs. Drown the engine in Diesel. This is a great degrease, second only to Whale Blubber. I'd advise blubber, but it's kinda hard to get nowdays thanks to the Greenies and if you did it is even harder to get in liquid form... That said, now manually rotate each piston through about four top to bottom cycles. Feel for ANY bind... and if there is a bind, stop the rotation! You'd better find the reason for the bind.
OK, now the Diesel is in the engine scrubbing all the gunk away, doing it's thing, now you gotta do yours. Pull the starter and the little rubber shield away from the clutch fork. Put the starter aside... and high pressure wash out the clutch area... get all the nasty muck and gunk outta there!. No, I'm talin' as high a pressure as you deem fit to wash out the area. You want to see CLEAR water comming out that case... If the exiting water is brown... keep flushing.
Now flush out the radiator and belt area real well. Drain the coolant and prepare to back flush the engine.... now's a good time to do a little maintance since you're gonna get wet an dirty anyway. Loosen the alternator belt and flush the alternator. When the alternator is good and dry, try rotating the pully by hand. If it binds, get a new one or rebuld the original. You might as well do it now, as 20 miles down the road. A bind means dirt, brushes, bearings or a combination is adding up to failure. If no bind, put the belt back on if you dare. Me, I'd take the alternaor to a autoparts store and have it bench tested to see if there were any damage.
Now for the starter. Inspect it! Has ANY dirt entered into the housing? If so you got a couple coices. You can do nothing, you can flush the starter, you can take apart, clean and reassemble the starter. It's your choice, I vote for the latter. Then take it to an auto parts store with the alternator and have it bench tested.
REMOVE EVERY electrical connection, clean it, air dry it and pack it with dialetric grease (spark plug boot grease). REMOVE ALL Grounds, and bunish the connections and reattach them.
OK, now most of the electricts are OK. Drop the Tank and drain it! Just do it, don't argue... just do it. Blow out all the fuel lines and vapor lines. Check your vapor canisters...thier probably toast if there was water in the tank...
Remove the exhaust system and examine it... you may need to drain it.
Drain the lamp housings.
FLUSH EVERYTHING with FRESH WATER... I MEAN EVERYTHING. If you don't people will say your Jeep stinks... and it will stink!
OK, now wait THREE DAYS! LET EVERYTHING DRY! Now you can get back to the engine. Use the starter to rotate the engnie. Look out, you're going to be shooting Diesel out the sparkplug holes... so stand clear. Let it crank no more than 3 seconds at a pop. Do it about 10 times.
Drain the deisel. Replace the filter and fill it full of fresh oil. Replace the plugs and see if it'll start. Now BTLT, here's where we need to know more about your rig. If it was carb'd I a had you rebuilding the carb, removing the intake and exhaust manifolds and flushing them... but you're on your own here!
If the engine starts... great. If not... fill out your profile an we'll go from there. My guess is as good as yours is if it will start.