The best way to shorten the shifter is to buy a quality short shifter. B&M makes great products for both the 95-99 5 speed (Isuzu transmission) and the 00-05 5 speed (Getrag transmission).
The cheap way is to take a hacksaw or pipe cutter and cut the stock shifter shorter. However, this only shortens the length of the stick, not the distance of the throw. To properly shorten the throw, you need to move the pivot point of the shifter assembly.
Here are some links to installation instructions for the B&M shifters:
