some minor gear chatter is pretty normal in most commodore manuals and is normal
best way to tell if normal noise is compare it to another car by hearing it.
low gearbox oil or incorrect oil viscosity will result in similar problems and premature wear of internals of box
if oil okay my guess is pilot bearing or throwout bearing
did you lube the shaft on installing throwout bearing? is it a new bearing? did you replace pilot bush/bearing on new flywheel?
this below from here
Clutch Troubleshooting
Abnormal Noises
Faulty clutch parts can make various noises. When an operator reports that a clutch is making noise, find out when the noise is heard. Does the sound occur when the pedal is moved, when in neutral, when in gear, or when the pedal is held to the floor? This will assist you in determining which parts are producing these noises. see below for what causes noise in different clutch pedal positions.
more useful info on clutches noise finding
HowStuffWorks "Common Problems and Other Types of Clutches"
An operator reports hearing a scraping, clunking, or squeaking sound when the clutch pedal is moved up or down. This is a good sign of a worn or unlubricated clutch release mechanism. With the engine off, pump the pedal and listen for the sound. Once the source of the sound is located, you should clean, lubricate, or replace the parts as required.
Sounds produced from the clutch, when the clutch is initially ENGAGED, are generally due to friction disc problems, such as a worn clutch disc facing, which causes a metal-to-metal grinding sound. A rattling or a knocking sound may be produced by weak or broken clutch disc torsion springs. These sounds indicate problems that require the removal of the transmission and clutch assembly for repair.
If clutch noises are noticeable when the clutch is DISENGAGED, the trouble is most likely the clutch release bearing. The bearing is probably either worn, binding, or, in some cases, loses its lubricant. Most clutch release bearings are factory lubricated; however, on some larger trucks and construction equipment, the bearing requires periodic lubrication. A worn pilot bearing may also produce noises when the clutch is disengaged. The worn pilot bearing can let the transmission input shaft and clutch disc vibrate up and down, causing an unusual noise.
Sounds heard in NEUTRAL, that disappear when the clutch pedal is pushed, are caused by problems inside the transmission. Many of these sounds are due to worn bearings. However, always refer to the troubleshooting chart in the manufacturer's manual.
