The rear gears on mine were shot when I took it in to the dealer for a tranny problem. As soon as they heard it, they told me they needed to be replaced (unfortuntely by the time I heard the message they had already put in the same gear ratio and I couldn't have them upgrade them at the same time
) With the ragtop, I couldn't tell the difference between the gears and road noise... good thing they could.
As for warranty issues, I would think that if you have a dealer put in FMS gears it would be ok, but I would ask them directly just to make sure.
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98 GT Conv: K&N, Pro-5.0