John, I had a similar problem with my '90 300E. I had installed cap, rotor, wires and plugs 10k ago. Problem was I mis-fitted the distributor cap o-ring and it caused an improper clearance between the rotor and cap which caused massive arcing. It only did it after a long drive and was not noticeable at speed. Symptoms sounded like yours. Check out the thread "300E misfire when hot" last posted around 12/6.
Chuck.