First we need to assume that all parts are out of balance to some extent.....
If the out of balance of the clutch, flywheel, driveshaft is aligned... . the total amount of out of balance will exceed the specifications, even though the single out of balance for any one item is fine.....
To index the flywheel, its removed and turned 180* on the crank... on those trucks that allow this... some flywheels only fit to the crank one way.....
To index the clutch cover... . remember the disc locks to the cover each time in a different location so it doesn't matter... . you un bolt it and turn it 180* on the flywheel... .
and to index the drive shaft you remove it and reinstall it 180* to the transmission... .
Its understood that each time the clutch engages and dis engages, the drive shaft is in a different relationship to the clutch cover... and flywheel... however this has shown to get rid of some vibrations... .
The above is outlined in failure analysis in HD truck applications..... for drivetrain vibrations... .
Jim