Your main resource is here:
https://www.sl113.org/wiki/ChassisBody/WindowsIn my opinion the uneven gap may be a question of adjustment and/or - there are light grey plastic inserts (clips) in all the jaws holding the glass that are responsible for holding the glass. This inserts inclue a plastic washer (originally orange) that acts as a shock absorber or, in any way, is softening the tension between the glass and jaw.
Another reason for rattling that I fixed last year was the A pillar seal being made of too hard material (original MB part).
I would have thought:
1. Check if all the jaws are glued to glass (and one of them is not lying down there inside the door)
2. Check and if need be correct the glass adjustment, observing the order: door fit to body, glass to hard top, soft top to glass. The procedure is in the Technical Manual quoted above.
3. Check the plastic inserts - if all of them are there and they are not broken.
4. (critical) check if all the orange washers are there and make sure they are soft
5. Check the adjustment of the force with which the inserts are contacting the rails (procedure in Technical Manual).
Quite frankly, if you were not doing anything with the inserts (clips) or orange washers for some years, I would just replace them all.
All the clips and orange washers are available at the dealers.
Orange washer (new part number!) A 113 725 00 99 64, 6pcs
Slide (insert, clip) left
front top A 113 725 09 34
front bottom A 113 725 05 34
rear A 113 725 07 34
Slide (insert, clip) right
front top A 113 725 10 34
front bottom A 113 725 06 34
rear A 113 725 08 34