Just finished with a couple week project of pulling the engine (Defender 3.5L) and gearbox (LT95) in order to replace some leaking seals. While I was at it, I replaced the clutch plate, cover and release bearing. Got it all buttoned back up and went to test drive today. Engine roared to life fairly easily and sounded beautiful. Truck wouldn't shift into gear, though. Pedal was very soft and went down too easily.

With the engine not running, I can select every gear with ease. There's a slight difference in the noise coming from the clutch with the pedal depressed. I climbed under and watched while my wife pressed the clutch pedal a few times and it looks as if the clutch release lever isn't moving much.

I bled (and bled again) the clutch. I suspect that perhaps the master cylinder and/or slave cylinders may have gone bad in the two weeks it was out of the truck. Both were replaced within the past year. I've ordered some new ones and will have a go at replacing them tomorrow when they arrive.

Any other suggestions of what it could be?
 
Sounds like air in the system then. Try leaving the pedal pushed down overnight? Or reverse bleeding?
 
In the end, I bought a pressure bleeder to force the fluid through the master cylinder. Before this, as I was pushing down on the clutch pedal the fluid level wasn't going down but the fluid was getting frothy. I think that the master cylinder was air bound and by using the pressure bleeder, it forced the fluid past that point and I was able to bleed as normal after that.

Once I got the system bled and the clutch was working again, I noticed that the bite point for the clutch was way down at the floorboards and the clutch engaged when I barely came off the pedal. Took the little cover off the top of the master cylinder and the nut on the rear of the pedal mechanism had backed completely off. This left a lot of play in the clutch before it did anything. That was tightened up and now everything is back to normal.
 

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