If the piston were pushed into the bore all the way. what would happen as the clutch wares?
The lever would get even closer to the grip with miles. I don't think the clutch on the FJR is self adjusting due to the fact it engages so close to the throttle. But again, I could be wrong.
The bottom line is with the clutch engaging so close to the grip, you can safely add a thin shim to the rod to push the engagement towards the middle, regardless if self adjusting or not.
The only way you could screw your clutch is if you're pushing on the pressure plate with the lever out, and you would IMMEDIATELY know that because clutch would disengage by barely pressing the clutch lever.
On a self-adjusting clutch like my BMW, if you were to shim the rod, it'd push the slave cylinder further in indeed, but as long as it didn't reach the bottom, you'd be perfectly fine.
As a matter of fact, my BMW had a master cylinder piston adjustment, and I adjusted my clutch outward because it was similar to the FJR, and I like to only use 2 fingers to operate the clutch, which means I can't use all the travel or I hit my fingers without disengaging the clutch. Using that screw that changes when you start pushing the master cylinder piston is the exact equivalent of shortening or lenghtening the slave cylinder rod (by their proportional distance, that is). I could start pushing the slave cylinder with that screw if I wanted; that's why you have to know what you're doing, and why the screw is loctited (and red) from the factory.
I don't understand what's the big deal here. We're dealing with mechanical stuff. If you push the rod too far, you'd know it immediately. If clutch engages in the middle, it's the ideal position. If it's designed as self adjusting, it'd always stay there. If not, you have more lever room as clutch wears. A non-self adjusting hydraulic clutch would cause the lever to move very little towards the grip throughout the useful life of the clutch. But that's not the case with a manual clutch, since without hydraulics, the mechanical advantage has to be much greater to have an acceptable lever pull, and has to be adjusted more often.
If somebody wants to do it, go ahead. As I said, I don't know this clutch so can't answer specific questions. All I can say is ALL hydraulic clutches operate under the same mechanical principle, and without a master cylinder adjustment (we don't have any), the only freaking way to adjust engagement point is by changing the rod. Just do it that it engages in the middle, to play it safe.
If even a small shim pushes the engagement far out, then it means it's a self-adjusting clutch with a badly designed ratio. The only fix in this case would be a different slave (smaller bore) like somebody already mentioned, or most likely, a master/slave cylinder combo, which I wouldn't even mess with. Only one easy way to find out. Later gang.
JC