Dan, I wouldn't worry about the short "throw" of the system. Even though you're at 1/2" at the end of the yoke, and the yoke is probably about a 2:1 pivot arm -- meaning your travel at the throwout bearing end is 1/4" (1/2 of the slave cyl. throw) all that's really necessary is for the throwout to depress the springs enough to move the clutch parts apart enough that they don't touch. That means 1/8" is enough, or even 1/16" or even less... Just enough that any runout of the flywheel/clutch plate system doesn't cause enough drag to rotate the trans shaft.
It's not unusual to expect the slave to have much more travel -- because your foot sure moves a lot under the dash when actuating the clutch. But there's a ratio there, too -- due to the pivot point of the pedal in relation to the actuation point of the clutch master.
The only adjustment I need to make on mine is to move the clutch friction point (with respect to pedal travel) a little higher off the floor. Right now, all the action seems to happen in the bottom 1" of pedal travel. (Might be a little more, but it's way down there.)
The most important bit is, of course, you're back on the road for the holiday weekend (hopefully!)
Ken
Upon reflection -- another possible source of throw "compression" may be the ratio of slave piston diameter to the master piston diameter. Are your old slave and new slave cylinders the same diameter? If the new one's bigger, it'll move less than the old one.