Well my wife's SLK350 roof started leaking again!
I dove into it trying to fix it and finally got it worked out.
i ended up adjusting the actual roof and windshield gap. Basically making the gap between the windshield and the roof more square/even.
Hope this helps and I think I over explained more than normal, but just wanted you to have as much info as possible!
Also, this could help with the E350 roof leak, I am sure the locks are the same and have the same adjustment