One problem related to manual transmission has been reported for the 2001 Ford F-650. The most recently reported issues are listed below.
Since ownership of the vehicle consumer replaced the clutch master cylinder seven times. Front axle was replaced once. While driving at any speed the gears were not shifting properly. Dealer replaced the old transmission with a new one.
| Clutch problems | |
| Clutch Pedal/linkage problems | |
| Transmission Failure problems | |
| Axle Assembly problems | |
| Manual Transmission problems |