My GT500 is also going to get this update. The only thing I notice, though, is friction noise from the clutch upon engaging with the driver side window down. Flywheel, clutch, input shaft and syncros. Does anyone know if there have been clutch or transmission failures prompting this much work? Some of the parts are presently on back order until February.
As I understand it, the initial production flywheel that was used in the GT500 was warping in typical stop and go traffic. When warped, the flywheel would not allow the clutch to properly disengage. This, in turn, could potentially damage the syncros. The Ford repair kit contains new syncros, I think, because of the possibility that they could be damaged, not because they are damaged in every case involving a bad flywheel. It seems Ford wanted to resolve the problem right the first time, thus the extensive replacement parts list.
I don't believe there have been any "failures" of the clutches or transmissions if you define a failure to be a completely fried clutch or blown transmission. The problem is indicated by poor engagement, creep and mildly grinding gears.
The friction noise you describe, if occuring when in neutral, is common and apparently inherent in the ceramic twin disk design. I've had the work done to my GT500 with excellent results but the noise persisted.