Craig,
There must be something, that all of us have overlooked.
If the system is hydraulically sound, and it has to be given new components, and no leaks, then it'd be handy if you could post pictures of your system from pedal to slave cylinder.
As for master cylinder stroke, the full travel of my clutch pedal translates to about 95 % of the master cylinder stroke. The Clutch starts to bite about 40% of the way up the pedal stroke. The action is quite digital, as the pedal is quite short (about 60% of the honda clutch pedal length at a guess).
John.
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