One problem related to manual transmission has been reported for the 2004 Ford F-550. The most recently reported issues are listed below.
Problem 1: in 2004 I purchased a new Ford F-550 with the gasoline v10. About one month after owning the truck the through-out bearing on the clutch started making noise and has done so. This year with only 49,000 miles on the truck now it does not want to go into gear sometimes. By the time I contacted my dealer he said that the truck was off warranty. Did they sell cheap bearings in these trucks, because my last f350 I had for 14 years without any problems. Problem 2: ever since I haved owned this truck. When you are sitting at a light and get ready to go. All of a sudden the engine shuts down for about 2 seconds and then goes.