PCM is in the engine as far as I know. the BCM is inside.
No, that's far from it. If everything is going dead as you hold it on start and it makes a CLACKING noise (as if the starter has power but the engine won't turn over) then it's a battery/alternator problem... and it can end up being both because alternators and water don't mix. The alternator on the Ecotec is in an odd position. It's under the throttle body... or at least, that's where the cables for the alt are.
If you hold the key on start for 10-15 secs, it should make a nasty sound which is reminiscent of a "clac clac clac clac" in fast pace. If this is true, it's the battery or alternator. This is of course, assuming the battery has enough juice to even flicker the lights. Sometimes, the car will just make a softer click noise and you can hold it forever in start, but you have no lights at all, not even the odometer will be on. I think this is the situation that applies to you. I have a feeling because you've had electrical problems before, you may have issues somewhere between the battery, the alternator, and the cables. I know the cables on my Camaro have acid corrosion all over the battery area because this car has gotten wet with coolant before by the battery area, and the previous owner didn't tighten the battery terminals right. I know have to figure out how to deal with it.
If you can source another GM battery, swap it and see what happens next. TAKE OUT THE SPARK PLUGS BEFORE ANYTHING... IF that water circulates through the engine, you will damage it. That way, if you can get it to crank and turn over, you can drain the water as well.
If you can't source another GM battery, then take it to a parts store and have the battery load tested. Pretty sure it's dead from what you say, but better safe than sorry.
Also, the fuel pump priming is NOT a clicking noise, it's a quiet hum that you have to be paying attention to when you put the car on the on position. The hum usually lasts about 5 to 7 seconds. You may have to have a friend put it on the on position and listen to it by the rear driver's side tire.
The fuel rail pressure relief valve is near the oil cap.
It's a schrader valve that looks similar to a tire valve stem. You can get a small flathead screwdriver once you take off the small cap and press the little pin inside of the valve in. Fuel should spray out for 3 seconds. If the spray is weak or very little fuel actually comes out, then you have a fuel issue as well.
Regardless of whether or not this is an issue, you should check the fuel pressure just to make sure it's not something serious, but I'm fairly certain you need to start with the battery first and go from there. If you do your own work, I would suggest testing the alternator as well. You have to get it out and take it to the parts store. They will tell you whether or not it's a good alt.
I should also mention, take out the relay for the fuel pump when you crank the engine to purge the water. You don't want to exchange flooding water for gasoline in this situation because then the engine will have a hard time normalizing and then you might fry your cat with all the unburnt fuel.
stockinteriors.com sells premolded carpet. You can also look for a used carpet in the junkyard.
If you want to play your luck, purple power and pressurized water. That might help. This of course would mean you taking out the seats and pulling the carpet out. I would also recommend changing the jute padding. They sell that at home depot. Just cut to size.