The flywheel should be resurfaced or replaced when replacing the clutch disk. Flywheels with scoring and hotspots are a common cause of clutch chatter. Clutch chatter is the sudden shudder that occurs when a faulty clutch disk or clutch component is initially engaged. This shudder or vibration may vibrate throughout the entire vehicle. It's often the result of worn or contaminated clutch components. This chatter is caused by the disc grabbing and releasing the flywheel and pressure plate as the assembly is turning. It happens very quickly as the engine is rotating.
A flywheel that has become out of balance will cause a vehicle vibration that increases with engine speed. Check for imbalance by revving a known good engine to 2500-3000 rpm with the clutch pedal depressed and feeling for any flywheel vibration.
Check with the vehicle manufacturer for testing specifications. It should be inspected for runout with a dial gauge mounted on the engine block. A flywheel with runout that is beyond specifications must be replaced.