99 Saturn SL- went through high water, won't start

On Monday we had a little hurricane here in Florida and some of the roadways ended up flooded. We ended up driving through about 2 feet of water at about 35 mph. You couldn't see it until you were upon it. About halfway through the 30 ft puddle, the car started knocking and was hard to accelerate, even out of first gear. After a block or so it accelerated normally and seemed to be fine. We drove about 7 miles and then parked and shut off the ignition for about an hour and when we started it up again the Service Engine light came on. We drove about 2 miles to the store, parked again for about an hour and this time while driving the car started lurching at around 50mph and the idle was running up between

2100-2600 rpm while sitting still. It seemed to hesitate quite a bit on acceleration. We got it home 9 miles and at that point the idle speed had settled down to around 800-900. We shut off the car and left it for over a day. Last night I started it up and let it run a while to see what it would do. It did run a little rough and the Service Engine light was still on but it never shut off. This morning my wife went to leave for work and the engine would not turn over. There is a weak whining sound then clicking. I can't tell if the alternator has shorted out and now the battery has finally died or what. Any ideas on what could have happened? (I had planned to take it to Auto Zone to get the codes checked but now since I can't get it started that's going to be a problem.)
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Weasel
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