2000 Volkswagen Cabrio Keeps Dying, Help!!

1 week ago I accidentally drove my 2000 Volkswagen cabrio, manual 75000 miles, through approximately 1 foot of water at 35 MPH.   The car died half way through the puddle and would not restart.  With the hood open and my wife cranking I noticed arcing from the coil wire back to a ground on the coil its self.  The car eventually started and I drove it home.   The next day the car died after 3 minutes of running smoothly, same problem; I waited and the car eventually restarted and I finished driving it home.  The car runs fine for the first few minutes or until the engine warms up.  When I hit the water I had only been driving a few minutes and the engine was still cool, so I don’t suspect a cracked head.  The car cannot be driven for more than a couple minutes at a time without dying, when it does die it is only when I shift into a higher gear and give the car throttle.   The engine sucked in significant amount of water, I have already changed the oil and dried the air filter, replaced all plugwires since the water accident.  Please help!!