Because you have a random misfire in two cylinders, and because you have an M104 engine produced between the yearas 1993-1995, my best guess is that you have a bad engine wiring harness. Misfires are one of the symptoms of the dread flaking wiring insulation problem.
Do a search on this site for "engine wiring harness" or "wiring harness", and you will find enough posts to keep you up all weekend.
The harness itself is about $500, and expect to pay 2.5 to 3.0 hours for labor at an indendent shop.
Be sure to go to an independent mechanic that specializes in Mercedes. They should be very, very familiar with this problem, and have surely replaced dozens and dozens of harnesses on 3.2 liter M104 engines.
2001 E430, Bourdeaux Red, Oyster interior.
1973 280SE 4.5, 170,000 miles. 568 Signal Red, Black MB Tex. "The Red Baron".