[RETed]

Replacing the pilot bearing is not an automatic eliminator.
In fact, just doing a clutch job which entails removing the transmission (i.e. input shaft) from the engine will actually increase the chances the pilot bearing gets f*cked.
You can kill a brand new pilot bearing by man-handling the reinstall of the transmission back into the engine very easily.
I've done it.

Signs of a failing pilot bearing:
* noisier with the foot off the clutch pedal - i.e. clutch pedal released
* With clutch pedal in (and all brakes off), car will stutter and creep forward, even though it's not supposed to.
* Shifting into any gear gets difficult; if you can shift into any gear with the engine off, then that eliminates a bad trans and makes it almost 100% it's the pilot bearing

You have basically described all 3 of the above.
This is why I suspect the pilot bearing.

The throw-out or release bearing really only comes into play when you step on the clutch pedal:
* noisier with the foot ON the clutch pedal


-Ted