If you have a Toyota Dealer Install the SC, your factory warranty is maintained. If the SC as especially hard on the manual trans, then I don't think Toyota would be selling it with warranty liability.
See my report at:
http://forum.ih8mud.com/fj-cruiser/2...er-report.html.
I had my local Toyota Dealer do my SC install and TRD CAI and TRD Cat-back at the same time. My dealer gives customers who bought their vehicle from them 25% all aftermarket parts. Here is how it broke down for me:
TRD Supercharger kit 3312
FJ Fit Kit 360
Labor 468
TRD Cat-Back 399
Labor 78
TRD CAI 319
Labor 117
It was worth it for me to have the extra power which I need with a set of larger tires and heavy bumpers.