Because of the location of the pivot, if you adjust the pushrod to establish pedal height without the pad, the rod length will be longer than it would be with the pad. Since the service manual was silent on that I had presumed that the measurement was with the pad in place. Hopefully you don't need to mess with switch B because that is going to be a world of physical hurt adjusting that Honcho s comment about removing the rubber cover is interesting. Once the distance C is set you go back and check the operation of switch A and adjust as described. If nothing is bent and the MC was reinstalled correctly and the switch A adjustment is not really screwed up then you should end up with the correct free play.

I think you need to follow the advice of Honcho and go through the adjustment procedure for the push-rod / locknut C to establish the correct distance C in the diagram then check your free play measurement. If hitting switch A is what is establishing the upper limit of pedal movement that is a serious problem. I can't go out and look at my car to confirm this because it is now in winter storage however, it seems to me that if you created some free pedal play by loosening locknut A and backing off the clutch switch, you may have just treated a symptom rather than fixing the problem. So should the clutch pedal be higher than the brake pedal from the factory and can the height be adjusted without affecting engagement ? I figure I would ask here before bothering the shop again for something that isn't a problem. I've thought maybe the clutch was already going but before the new cylinder it had some freeplay in it. One other thing i notice now is there is no real freeplay like other clutches. I did compare it to my s2000 which its clutch pedal is also higher than the brake pedal but its considerably old and has a bunch of free play. I've always had the steering wheel rather low but never remember bumping. The clutch engagement doesnt feel any different but when I let the pedal its definitely more 'springy' and returns frimly but I sometimes bump the bottom of the steering wheel with my leg. Ive had the car for about 7 months and put 4000 miles on it so I never knew what it was like with a new clutch cylinder. I had both the Clutch master cylinder and slave cylinder replaced on an 2005 NSX and it seems the pedal is taller than before, but I am not sure if its because the old Master Cylinder hydraulics were starting to fail and the factory position should be higher as it is now.

Honda s2000 clutch pedal diagram