Driveshafts and harmonic balancers are a lot easier to check and replace than the flywheel. If the driveshaft is mis-aligned/unbalanced then you will definitely feel the vibration in the shifter. Put it in neutral and rev the engine. If you still feel it in the shifter, it's not the driveshaft. Check the balancer for rubber protruding anywhere around its edges.
If you recently had a clutch install done and the flywheel wasn't balanced correctly then you're about to have a pile of fun.