Concerning the Bolts. There is different sized Flywheels. I don't know if that means the Clutch Bolts might be longer or shorter on some Flywheels or not.

Also do you have a 300D Flywheel in it or is it a 240D Flywheel?

There should be another Plug up higher for filling the Transmission. You fill it until Fluid/Oil starts to run out of the upper Plug Hole.

On My Diesel Volvo there is 2 Pins in the Flywheel. There is corresponding Holes or Notches in the outer Sheetmetal Housing of the Pressure Plate that those Pins must go into or it would indeed be out of Balance. However, in the Pics I have seen of Mercedes Flywheels I have not seen any such pins on it.
No have I seen on the USA Made Cars I have owned that had Manual Transmissions.

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84 300D, 82 Volvo 244Gl Diesel