The ideal short shift kit has a short upper half and a long lower half...That is the combo that will produce the least amount of travel by your hand. However, lenthening the lower part of the shaft screws with the internals of the transmission...I'm not an expert about that so correct me if I'm wrong.
...here's what happens in basic physics. We'll asume that the lower part of the arm is equal. When the upper length of the rod is shorter, the amount of torqe (produced by your arm) required to move it is greater. Its just like a car jack. Its easy to lift the car when using the far end of the jack, but try pushing down from half way and see how tough it is.
Even though the short shifter requires more torque from you, the force on the other side of the ball is equal to a long shaft except for one thing...MOMENTUM. When you have to push the shifter hard, you are more likely to slam it into its farthest position. Its this slamming that can wear out the forks on your transmission. With a standard shifter you (well at least I) are just guiding the stick into the right position and letting it stop where it wants to almost effortlessly.
If you get used to the travel length of a short shifter it won't be so much of a problem...in fact I doubt it has ever cause a problem that didn't already exist from the driver's shifting style. But if you are acustomed to moving the shifter hard, then a short shifter will aggrevate the situation. A tip is to never grab ahold of it. use the palm of your hand with your fingers relaxed and you'll be ok.