slimwiltataz ...................its the bearings on the input shaft allowing the shaft to wobble that make the noise .
Your gears will be fine if you get the bearings done ASAP . The noise dissapears when the clutch is on the floor because that is the only time the gearbox input shaft stops spinning . The reason you only hear it in neutral is that when in gear the vibration / knocking is absorbed by the engaged gears and goes up the output shaft to the diff and drive shaft . In other words ....... when in gear the input shaft has no room to slap about on its worn bearings ........ the gears hold it tight .