Update/Correction. It seems I was so shocked by the prices they were quoting me that I got it wrong, but it is still way high IMO. I was quoted $2200 for just the top transmission, hydraulic push rods, drip tray, and calibration of the assembly. The $5500 was the total (not in addition to the $2200) to add replacement of the wheel wells. I told them not to do anything. They still charged me $290 (2 hours of labor) to diagnose the problem. I won't be going back there.
The way he explained it to me when I picked the car up was that if the motor keeps going beyond the proper end points, because it is bolted to the wheel well it will torque the whole wheel well and bend it out of shape. He went on to say that in extreme cases he has seen it bend quarter panels. He advised that spending the initial $2200 would be a band-aid approach and the problem could come back because of the wheel well problem. $5500 is still outrageous to me.
Needless to say, I will be taking it to an independent shop for a second opinion.
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