First check the motor mounts.
Check the flywheel again. Turn the bolt slowly, looking far any out-of-round condition. You may want to retourque it and also make sure the keyway is in position. Lift it with a prybar and see if there's any movement in the crank. Slowly reverse it looking for noises which would indicate rod bearings.
Then check your clutch basket. The fact that it only occurs under load and in gear suggests something in the rotating assembly has gone south.