Your saga got me thinking.................
...........I've got a 313, too, and mine has done the low speed jolt/bunny-hopping ever since I have had it - it occurs as you open the throttle, for example as you turn into a side road off the throttle and open it again. I have been fed all of the "they all do that, sir" lines from the dealers, too!
So tonight, I decided to do the 'throttle pedal released position reset' and 'throttle valve closed position reset'. It seems to have completely cured the jerky throttle response - its like driving a different car!
Could it be that the dealer has done the reset procedures above to your car, and that is why the bunny-hopping is better?
If your vibration is road speed related, not engine speed related, it seems very unlikely to me that it could be caused by the flywheel, or the clutch for that matter! I think you are probably on the right lines with wheel/tyre balance, prop-shaft, rear axle etc. i.e. something after the gearbox, but maybe they should also check the gearbox itself.
Good luck and keep us posted!