Toyota Repair: 2007 Toyota Avalon - Clogged sunroof drain, 2007 toyota avalon, release latch

Question
Ted - I read many of your replies dealing with clogged Toyota sunroof drains and have a similar situation I would like your advice on.  

Over this past weekend, during a heavy rain, I was unable to open my vehicle with the remote device.  I used the manual key to get in then attempted to start the vehicle.  It started but when I shut the engine off, the headlights remained on and the cooling fan continued to run.  After several attempts at starting and turning off the engine, I was still unable to turn off the lights and the fan continued to run.  Further, many warning lights on the instrument panel were lit and the navigation system was  negative (black was white).  When I opened the hood release latch to disconnect the battery, I noted water in the hood release latch.  I also noted that the A-pillar and speakers on the driver's side were wet. When I went outside and opened the hood, water came out of the hood when it was lifted.

I had the vehicle towed to my dealer as the vehicle has only 22k miles and is still under warranty.  After they had inspected the car, they indicated that the sunroof drains had been clogged which caused the flood.  They also stated that they normally charge to clean this, but they would not in this case.  After reading your replies to similar cases, this is not a simple problem and in fact Toyota has a special tool to clean out this drain when it becomes clogged.  Their response seems to minimize the difficulty of correcting this problem. What do you think?  I am also puzzled by how water would get into the hood - this never happened before on any other car that I owned.

My biggest concern is the water damage to the electrical system.  Everything I have read about this points to serious problems with the vehicle, maybe not at first, but down the road as the corrosion starts.  (In fact, my insurance company indicated that a car can be totaled from water damage, even if not submerged in flood.)  Although the dealer said my problem was resolved and asked me to pick up the vehicle, I told them I wanted to review this with the manager since I was concerned the vehicle was not safe and that I wanted them to buy the car back from me.  They arranged for a regional rep from Toyota to come to the dealership to discuss the situation with me.  I have not yet had this meeting.

I would appreciate your thoughts on the risks I may have in taking the car back.  
1. Can/ did this leak cause permanent damage to the electrical system that will worsen over time?  
2. Can/ should the parts of the electrical system that got wet be replaced?  (I am not sure exactly what that would be, a circuit board, a computer).  
3. Is the water collecting in the hood related to the clogged drains?  If not what caused this?
4. What should be done by the dealer to rectify this condition and repair any damage?

Thank you in advance for you advice on this problem, I really appreciate it!
Fred

Answer
Since I'm not real sure exactly what is going on here and the fact that the car is still under the warranty my advise would be to wait for the factory rep to come and discuss this with you, any advise I would give you would be speculative and hypothetical, the only thing that I am sure about is that a sunroof leak/clog can not cause water to enter under the hood it can only leak into the passenger compartment, I'm sure that the field service tech can resolve this concern to your satisfaction and instruct the dealer what course of action should be taken.