The flywheel, clutch disc, and clutch cover are balanced as a unit. Assembling it wrong could cause vibration fro minor to catastrophic. Opening it up after installing is a PIA. Safest path is to take the three parts to a good balancing shop.
BTW - the same is true of all the other rotating parts. Crankshaft, rods, and pistons are also balanced. Also the drive shaft is balanced and should be checked if it was not marked on disassembly.