One problem related to manual transmission has been reported for the 1998 Toyota Tacoma. The most recently reported issues are listed below.
When accelerating in 2nd gear there is a bad vibration(2000-2500 rpm). It also "clunks" when shifting from 1st gear to 2nd gear. The higher the rpm the worse it "clunks". Vehicle purchased in November 1999. Taken to dealer twice regarding problem. Dealer says it is "normal". I am concerned that the transmission synchronizers are worn out and want to get problem resolved while covered under 60,000 mile drivetrain warranty.