There isn't really any linkage to speak of for the shifter (that you can mess with anyway). The seat for the shifter can sometimes wear out or disintegrate, but that just makes for a looser/sloppy shifter, not the problems you describe.

The MT-90 might help a tiny bit. And aside from making sure the clutch pedal height/freeplay are adjusted properly and the bracket is OK, I don't think there's much else you can do.

Also, you can make sure the clutch is disengaging by gently pulling the shifter towards reverse until you just hear the teeth start to "grind." Then start slowly pushing the clutch in until the grinding stops. It should stop (clutch completely disengaged) with the pedal about 1" from the floor. And no, it won't hurt anything if you are gentle and use common sense (no need to do it for hours on end, etc.). I don't remember which manual I got this one from...