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I have a 2001 F-250SD, 5.4L w/ the ZF 5 speed manual box, and 125k on the clock. My question pertains to the clutch/slave cylinder. When I shift gears, the clutch pedal does not always return fully out. There's no slipping in the clutch, so that leads me to believe it's the master/slave cylinder. The clutch is the factory clutch.
Winter/cold weather it seems to be more pronounced, but not always a problem. Under hard accelleration, it's about 75% to return fully out, but under normal driving, it almost always requires a toe under the pedal to "lift" it up fully.
Summer/warm weather, it's not nearly as bad, requiring about 20% of the time lifting the pedal out under any condition.
If you have water in the line (brake fluid absorbs water) then it could be freezing causing the slow return. I had a truck that did that, but I moved to a warmer climate instead.
Try bleeding the clutch until you get fresh fluid coming out of the bleeder.
If that doesn't help, you may just have a weak return spring on the clutch.