Not saying the process will be simple or inexpensive, but the OP’s Prizm can certainly be restored to the way it was before the flood. It may not make sense $$-wise if the OP has to pay someone else to do all the work required, but if the OP wants to diy’er most of the job, it’s something that can be done. Any electrical connection that corrodes can be cleaned or the contacts replaced.
Thank you all for the support and encouragement. Here is an update. I was hell bent on getting the car to work without taking it to a mechanic (not because I was trying to be cheap, I am between jobs right now and didn’t want to spend money that I am not making). The irony is that I haven’t done any car-related work before, nor do I have the right tools.
I watched some YouTube videos of starter removal on similar model cars and borrowed some tools from a relative and took the starter out. I had to use some extra leverage to get it out. However, I did not remove oil filter or radiator hose, like how some guys on YouTube did.
I took apart the entire starter. I saw corrosion inside (there were salt crystals formed inside). Some of the parts were stuck, which I washed with a degreaser and hot water. I also cleaned out all the copper parts with sandpaper and a knife. Made it look like new.
The part of this job that got me all confused was a stuck bendix. I saw videos of other denso starters been repaired, but they didn’t look like mine, so I had no clue on how to get it unstuck. I sprayed plenty of penetrating fluid and started wiggling the bendix like crazy, hoping for something to happen. Finally, the bendix assembly came off. It was stuck inside. I greased everything and put the starter back. And, it worked!! I thought, one down and plenty more work on the car to come. At least I got to crank the engine.
I also removed the computer, opened it up, washed the circuit board, dried and put it back on the car.
With the spark plugs out, I cranked it and water came out from only one cylinder. It is still a mystery why only one. The other cylinders were completely dry. The only possibility that I can think of it is through the air intake. But, how did water get only in one cylinder? Any leak possible? I cleaned as much of water as I can with a rag and sponge at the end of a long thin rod (like getting out ear wax). Occasionally, I would crank the engine. I repeated this till the rag came out clean. I sprayed some MAP sensor cleaner in to the cylinder and kept cleaning. Finally, I said a prayer and put the spark plugs back and started it. The car started up like a champ without even a hiccup.
By the way, I replaced the engine and transmission oil too. There was plenty of water pushed out from the muffler. I let the engine run for only a few minutes, just enough to get it hot so that any water that is still in it might evaporate out. I didn’t want to push my luck for one day.
I know that I still have more work to do on the car before I start driving it. I intend to get under the car and pick out any twigs that got lodged in the exhaust. I don’t want that catching on fire.
At least, I know that the engine runs. And, there is at least a sliver of hope of saving the old car.
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Congratulations, and thanks for letting us know. May your perceptiveness, patience, perseverance and a little luck continue to yield a good result!
Good for you. Getting the engine to crank and idle is an important step, b/c the heat will help dry the rest of the parts out. The sooner everything is dry, the less work you’ll have. The reason water only went into one cylinder might be that was the only cylinder that had its intake valve open when the engine was last stopped. The valves in each cylinder are opening and closing , sort of like a slot machine when the engine is running, and when you turn it off, whatever configuration it is at the time, it will stay that way. I like your can-do way of thinking. One tip for cleaning corroded electrical contacts, works especially well on flat connections like the photo below, try a pencil eraser.
GeorgeSanJose, thanks for the eraser tip. I remember long time back, I destroyed an electrical contact on a pcb by cleaning it with sandpaper and a knife. I learned not to do that from that experience.
Your explanation of the valve staying open on one cylinder makes sense. But, a curious question: Aren’t cylinders paired in a 4 cylinder engine? Shouldn’t two cylinders have open valves in that case?
I can smell some burning smell when the engine was on. Not the electrical type burning though. I hope that I was just being paranoid.
I’ve heard of folks using fine grit emery cloth for cleaning corroded electrical contacts. Regular al-o2 sandpaper that you’d use for sanding wood, not so much. For cleaning commutators and armatures, there are commutator stones available. When you use those products you have to be sure to remove all the leftover grit. There’s a CRC contact cleaner spray product I usually use as a first attempt.
Maybe there’s a catfish cooking on the exhaust manifold? 
If two valves were open, the water might tend to run down the cylinder closest to the throttle body and never make it to the second one until the first one completely filled up.