You need to check all the drain holes for the vehicle. As you already found one blocked front hole you need to check the other front one also. In the rear there are two drain holes located underneath where the convertible top folds down. These drain down just in front of the rear wheels. You need to follow the procedure to place the top in the service position and the drains are located one in each corner. Also check the rubber tub has no tears in it which also allow water entry to the cabin.
The module under the left seat is the main computer controlling most of the vehicle. The water will have shorted out the electrics, thereby causing the erratic widow operation.
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