I had a similar problem with my 1997 E300D .... it would run fine but stumble around 2500 rpm. After messing around with the flaps and all the vacuum control valves in the vicinity of the air cleaner, I eventually discovered that the electric change over valve that is attached to the underside of the intake manifold and controls the two flaps wasn't working right ..... it leaked vacuum. I never quite figured out exactly what caused the stumbling but I knew the change over valve was bad so I replaced it and the problem was no more. I suspect what was happening was that even though the flaps worked and didn't throw any codes the vacuum leak at about the time both flaps were activated pulled too much vacuum away from the other connected systems and probably screwed up the main intake flap control (flap up stream of the EGR) causing the stumbling. At least that is what I suspect. Any case replacing the electric change over valve for about $90 solved the problem entirely. Good Luck.