When the roof is closing and it stops does it make a juddering noise or is it quiet. First of all open the roof fully and check that the guide rails on either side are free of dirt, use a paint brush and WD40 and use plenty of cloths to prevent dirt splashing every where. I have a '96 E-class but I think the roof mechanism is very similar. If the roof make a juddering noise this is not so good. The motor is located above the left rear wheel in the boot. The mechanism consists of a toothed cable driven by the motor through a pipe guide to the rear of the roof panel. You will have to disassemble this motor and gain access to its drive gear in order to clean it of metal shavings/debris and to re-grease it. It is a very frustrating job and one that may wish to leave to the Mercedes experts because even having rebuilt the motor there is a real knack to adjusting it. If the roof is just coming to a stop and not making any noise then you in luck. Locate the motor and the large central nut on top is the clutch adjuster. Tighten it by 1/6th of turn and try to close the roof again. Keep adjusting the clutch tighter until the roof closes. If you hear juddering noises, immediately slacken the nut off and the above notes will apply.
Just remembered I had submitted a similar fix about a year ago and dug it out for you:- The motor is located in the recess above the near side wheel arch and is mounted on a small frame held in place by two 10mm bolts. In order to remove the motor you will need first to extract the sunroof cable that runs though it. What follows sounds complicated but is quite quick and easy. 1) Ease the sun roof back to half open, if the motor is not working just put a 17mm socket on the nut in the centre of the motor and hand crank it open. 2) Between the sliding metal roof and its headlining panel , about 10cm from the leading edge, are 4 pop connectors. Slip a large bladed screw driver between these and separate. 3) Ease the headlining panel forward and pull it up and out through the sunroof aperture. 4) Now close the sun roof, if necessary using the same hand crank method used to open it. 5) On the under side of the sliding roof panel at the rear in the middle you will see the end of the cable tube guide . Mounted at the end there is a metal butterfly mount located with two 8mm bolts. This mount is what actually holds the end of the cable to the sunroof bridge mechanism. Remove these two bolts and withdraw the whole cable forwards, again the hand crank can help here. Take care this cable will be filthy. Check the end for signs of teeth missing - if so replace and clean the motor gear box of metal shavings 6) Returning to motor - disconnect the electrical connector block. 7) To the front of the motor the sunroof cable tube is held in place with a clip. Push the tube end at 90 degrees to the motor body towards the outside skin of the car to un-clip and to disengage it. 8) to the rear of the motor you will see a similar exit cable tube. This time the the tube must be pulled at 90 degrees to the motor towards the car interior and when unclipped this needs to be moved away towards the rear to clear the motor assembly. 9) Once the two 10mm frame mounting bolts are removed the motor can be extracted 10) Check the health of the (replacement) motor gear box by removing the three 8mm bolts holding the steel backing plate in place. The large plastic driven cog can be removed by undoing the 17mm nut on the other side whilst holding the central spindle with a 6mm open spanner to stop it rotating. 11) Clean everything to a shine and re-grease liberally. 12) Reassembly is the reverse of the above remembering to clean the drive cable and re-greasing prior to reinstallation
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