One problem related to manual transmission has been reported for the 1999 Volkswagen Passat. The most recently reported issues are listed below.
Car has been back to dealer over 12 times for clutch related problems. Clutch stuck to floor, slave cyl leak, clutch replaced twice and slave cyl replaced three times. Leak destroyed inside dash, dealer ref to fix. Electrical probs in dash, crackling noise heard. Brake line and slave cyl problems. Persuing lemon law (suit filed).