I've got a '99 with a 4.6L and a 5 speed manual transmission. Fifth gear has a clatter that speeds up as the truck goes faster. Its easy to hear when in gear #5. When I shift into #4 it gets much quieter and I can only hear it with the heater off. I suppose I am looking at pulling the tranny and messing with the gears. Any one have any other ideas?

 

I have no idea if the problem still exists or not, because I no longer know anyone with a manual transmission in a pickup, but, Ford used to have a lot of issues with the input shaft bearing going bad prematurely. Might still be the case. Any TSB's regarding that ?

Dave