[Cloudsurfer]

Well, in an ideal world, you would balance the rotating assembly, which includes the flywheel, which can only be done while building an engine. Supposedly Porsche does this to every new motor that leaves the factory.

You can balance the flywheel and clutch setup off the motor. As to the engine internals, most any German build motor is pretty damn good on tolerances. Not perfect, and you can do better, but pretty damn good.

Any good flywheel that you would buy should come balanced. As to your dual mass unit, it is entirely plausible that it is worn. The two masses are held together with an elastomeric coupling, which can weaken or fail over time. If you're doing a clutch job, you'll want to change the flywheel anyway, as you can't reliably re-surface a dual mass unit.

If it were my car, and you have enough miles to warrant a clutch and/or just want to get in there and remedy your IMS bearing, I would pull the gearbox, update your IMS bearing, change the RMS seal, and do a clutch job with a new flywheel, balancing the clutch/ flywheel assembly before installing it.