I noticed that the S4 clutch release (throwout) bearing is a different part number between the S4 and S5 tranny's. Anyone know what the differences are *(besides the ~30% increase in price)?

 

I assume you're talking about the OEM ones? The clutch disks are also slightly different between S4 and S5 TII. http://www.mazdatrix.com/f86-92tb.htm

But all the aftermarket kits are intended for '86-'92, so I would assume Mazda changed some small, insignificant thing.