Engine running rough and no one knows why
As for reducing future carbon build-up issues, the simplest option is to add a oil catch can setup to the crankcase breather system. You also need to used a bit more high rpm/high load driving occasionally to minimise carbon build-up whilst it's still soft.
If you're looking for a more complete solution you can look at blocking off the EGR flow/disabling it. I would look at the UK MB tuners or some of the Jeep forums as they do this mod more often then you would find in an American MB forum.
EGR isn't normally an issue, it's the huge quantity modern diesels compared to older diesel engines as they now use it to aid engine warm-up, reduce engine noise under light loads as well as for emission reasons.


