TCS ABS Drained Battery Runs Rough Loses Power Electrical Problem Shaker 500 2007 Mustang V6 Conv

I have had my car 2007 Mustang V6 Convertible since Dec 2011 (bought used). Few weeks ago I noticed my Shaker 500 CD changer was making noise even with the car turned off. A few days of this and the car wouldn't start. I jumped the car and it started right away. I would drive the car for a bit and the TCS light would come on, the radio would pop and go to a different station and the car would run rough. This went on for about a month. Looked up forums on the problem and it stated the Shaker 500 was to blame. I replaced the stereo with a Sony from Crutchfield.com Car ran perfectly but still had to jump occasionally, I guessed I just killed the battery as I had to jump it every other day with the Shaker 500 (probably around 20 times) Went to Walmart & they replaced battery under warranty. Today has been 6 days with new battery and not one problem until this morning. Car started up fine. A few miles down the road the TCS AND the ABS light turned on. Car was running fine. I quickly turned off radio, a/c and the TCS & ABS lights stayed on. Car began running a little rough then the headlights turned off. (It was 6 am still pitch black out) I continued driving anyway as I had to get my son to school. I changed lanes and used the right blinker which worked, but then would not turn off. So I pushed the hazards hoping both signals would turn on and stay on, but they didn't I flicked my high beams on and it worked and my turn signal turned off. Then my lights turned off again. I dropped my kid off at school and headed back to the house. I kept turning the headlights on and off they would sometimes turn on, but then quickly turn off again. After about a total of 10 miles, my car really started to run rough as if it was going to stall. I stopped at a traffic light, put car in neutral and revved the engine. When I put car back in drive and hit the gas as normal, the whole car shuttered and acted like it was going to die, so I backed off the gas a little and it felt as if it jumped into gear and went on. It still felt as if the car was running rough though. I checked the radio, it wouldn't turn on, the windows wouldn't roll down, so I continued driving the last 5 miles back to the house. A 1/4 of a mile from my house the car shut off, no motor, no power steering, I coasted into the drive way and turned the key to off even though engine wasn't running. I put a charger on the car and that is where it will sit until I can check it again.
A few months back (say 4-6 months ago) it rained hard. I drove my car through high waters, up to the door jam. A few miles down the road and water began to POUR in from the passengers side front seat, flooding the inside of the pass side of the car. When I got home I parked in garage and let it dry. I pulled the plug on the inside of the engine compartment by the firewall and removed the leaves and junk that clogged it. I assumed found the culprit that had made my car flood. It never happened again, but my fuse panel did get wet during this occasion. It all dried with the help of fans and it never seemed to have a problem since. I just checked the plug today and it is free from any leaves or junk. The fuse box panel in the pass side is dry and looks intact. Here is link to the water pouring in floorboard (video) COPY & PASTE it
https://www.facebook.com/photo.php?v=10202009495299245&l=4524138140273600785
Any suggestions?