So I took the car in today, since it's a holiday and got the bad news. There is a leak somewhere behind where the convertible top stows in the body. The mechanic was able to get it to leak by dumping water on the area where the top meets the body just in front of the trunk lid. Now here's where it gets worse...there's rust beginning to form at the bottom of the spare tire well where where the water stood stagnant.
So here's what has to happen. First the car goes to the upholsterer to get the top removed (dealer doesn't have the expertise). Then back to the dealer to confirm where the leak is occurring. The leak will be welded shut by another outside shop, the trunk needs to be repainted and/or the rust areas treated. Then the top gets reinstalled. Fortunately, I'm out of town for a week now so don't need the car.
And guys, the dealer confirms that this is known issue for the '05 convertible. Ford believes there were defective body welds causing the trunk to leak. So all of you convertible owners out there should pop the trunk, remove the mat and tire, and check for any tell tale signs of water damage.