Help with strange clutch/transmission noise

[blinnbuc89]

I searched in the forums but could not find anything good on this.

Sorry this is kind of long, but it should help to keep from questions being asked.

First off, about 2 months ago I would hear this loud clicking noise coming from my transmission/clutch/bellhouse when i would stop with the clutch pedal out and idling in neutral. I took it to a reputable local shop who determined my clutch and throw out bearing were toast. They replaced clutch kit, fly wheel, and slave for a cool $936.
Now, about a week after the repair i would get this loud clicking noise when in neutral stopped idling when the clutch is released. If I push the clutch in, the noise will go away. the noise is similar to a loud knocking engine, or a bad/stuck rod/valve, which I thought it was at first, I immediately got mad and thought the clutch is a waste of money, now the engine is going out. the engine has 170,xxx miles and runs like a top. I maintain vehicle and it is nearly perfect.
The shop now believes it is either a input shaft bearing or output shaft bearing, I can not remember, but the clutch is still under warranty for 12 months/12k miles from purchase. is this something they should cover or am I SOL? or are they wrong and the clutch is messed up or installer improperly?
Thank you and sorry the post is so long.

 

[blinnbuc89]

By the way, the truck is a 99 b2500.

 

[Hotrodlincoln]

Sounds like the Input shaft bearing. They should have checked end play on the input shaft when there was access to it.

Drain the oil from the transmission into a clean white or clear container and check it's condition. If it comes out grey or silvery it's a bad bearing. If you get big chunks or shavings then it has bigger problems.
Either way, it needs a rebuild or replacement with a known good trans.