Ive had a terrible rattle noise when at low rpms in every gear for about 6 months, or engaging the clutch. When I pulled my trans, the pilot bearing was all torn up and resulting in scoring of the input shaft. Does anyone know if this shaft rattling for so long would damage any other parts of the transmisson or should I replace it and hope for the best. All the bearings look ok in the trans.

 

If it made noise while the clutch was FULLY ENGAGED, then there's something else wrong with it. Think about it: the only time that the clutch gear (the correct name of the thing that a manual trans has sticking out the front with the splines on it, it doesn't have an "input shaft") is spinning in the pilot bearing, is when the clutch is not fully engaged (partially or fully disengaged). Therefore, if it makes noise when the clutch IS engaged, it's not the pilot.

More likely, the noise is coming from the countergear bearings, or the gear teeth. A VERY SMALL amount of wear on those teeth will make all kinds of racket. And, if the clutch gear teeth are damaged, so are the countergear ones.

Not good news, I know.

But yeah, you can buy the clutch gear along with its bearing and selective-fit shims and change it out, and replace the pilot, and hope for the best. Just make sure you get the rollers and the Torrington and the keys all back in there right, and get the clutch gear bearing preload set right; and see what happens. Experience tells me however, that it's not likely to be good.