Where the linkage connects to the transmission level the little ball stud is adjustable in the slot of the arm. If you know which way it's off you just need to move it a 1/16 - 1/8 of an inch in the slot and it should do it. There is an actual method of doing it since the shifter has some holes you put a pin (or drill bit as said above) thru and then set the linkage at the trans. to neutral.
But you can usually just bump the adjustments and get it close.
Make since. You just have to think about which way you need to move the ball stud.
Here is a pic of a 5sp. You can see the ball stud nut and the slot it's in.
[This message has been edited by Dodgerunner (edited 02-08-2007).]