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.)