One more thing--make sure the clutch is well bled. You may be aware that these are notoriously difficult to bleed completely.
It's important to remember that, as long as the clutch is well bled and of course not leaking, the hydraulics aren't the issue any more. A certain amount of movement at the MC will give a certain amount at the slave. End of story. The rest of the mechanics are the issue. Anything that limits movement, like looseness, can be the problem.
I had this problem for years, and finally solved it after thinking it all out correctly. My clutch (err... my CAR's clutch) now engages very nicely in the middle of its travel. The key was to get the pedal stop in the right place--the shop manual provides very little guidance on this.