One problem related to manual transmission has been reported for the 1998 Volkswagen Jetta. The most recently reported issues are listed below.
First incident with gear shifter happened in March 1999 when it popped out of first, third and fifth gear while driving. The gear shifter rattled immensely. The second time, it had been hard to get into first and third gear and was popping out of first gear in particular. Prior to having the car fixed, it was parked in my driveway during a storm. The car popped out of gear and rolled down my driveway into a tree. Volkswagen adjusted the shifter (which they adjusted incorrectly in the first place). The third time, (which is now) it's very difficult to get it in first gear.