Problems after driving in the rain

After I got in town today it started pouring down rain really hard, and teh streets were literally flowing like rivers it was coming down so hard. I went through a couple puddles and got my engine pretty wet(no water in the air box, I did think to check). It wasn't a purposeful splash, but it was deeper than I thought(up to 6in in places) I know this isn't as deep as the creek I've been in, but afterwards I shut my Jeep off to unload the engine from my Jeepster and when I went to start it back up, it kinda stuttered, and idled/ran real rough for a couple minutes. It kinda scared me as I haven't had that happen before(and I'm 130 miles away from Olathe, and the last $400 of my check doesn't become avalible until tuesday, so I dont want to be stranded here). Any clues as to what it could be that happened?

Sounds like what happened to me after hitting a deep mud puddle last weekend. It turned out to be very minor, though. Look inside your distributor cap. If it's wet, spray the inside liberally with WD-40 and replace. Easy fix, if that's the problem.

Thanks!! I will check that.

The first thing to do is dry out the coil to cap wire, pull the boots and dry the insides out as well as you can. If that doesn't help pull the cap off and dry out the insides of the distributor. Hair dryers or compressed air work well for this. Might as well check out the plug wires next.
If the filter got wet, it will shut off the air flow. it doesn't have to be soaked, just wet enough to close the pores up.
In most of the Jeep distributor caps there is an air vent. The identical Ford cap doesn't have the vent. Water will run in the vent as well as seep in around the base of the cap.
WD40 and other sprays help displace the moisture, but in my experience can cause troubles of there own sometimes. WD40 is fairly resisitive, it likely won't hurt the high voltage circuits much, but is ill adivised for most anything else.

Steam build up gets into everything and turning it off started to cool down the engine, engine compartment and components where that steam condensed. Mostly if you kept it running for an hour or longer it would have stayed hot and cooked off/evaporated the moisture and you probably would never have noticed it. But yea, it needs to either dry out or be dried out...