One problem related to manual transmission has been reported for the 1999 Jeep Cherokee. The most recently reported issues are listed below.
The dealer said they have seen this problem in many wranglers with the same clutch and transmission. The throw-out bearing has rotated on the clutch fork and the fork has been pushed down over the throw-out bearing, causing the clutch slave to extend to the maximum, which causes the clutch not to be able to be depressed. Therefore, I was driving down the street with a non-operational vehicle. This was a dangerous situation.