One problem related to manual transmission has been reported for the 1998 Toyota RAV4. The most recently reported issues are listed below.
On numerous occasions over a two week period, the manual transmission pops out of 5th gear without warning. This leads to a very dangerous situation when in traffic as it causes the vehicle to reduce momentum rapidly and could be easily rear-ended. The last event occurred on 6/7/2007, the day before vehicle was repaired by a private garage. I have asked Toyota for assistance on this problem, but was declined. They have a service bulletin out on the problem, but the coverage is not adequate. This problem can occur at anytime after their coverage expires.