I wonder if the OP ever sorted this out?

I have a very similar problem with a 2002 E320. Rough idle that seems to be a random misfire. Worse when the engine is warmed up.

About a 1K miles ago I had a CEL. Code indicated drivers side upstream O2 sensor. Although, I didn't notice the rough idle at that time and the car seemed to run fine.
Prior to replacing it I noticed the idle degrading.

I replaced the O2 sensor and reset the CEL, rough idle remained. The car has roughly 142K and not knowing when the last time the plugs were replaced I figured it would be a good time.

I used NGK 7090 plugs which appear to be very close to the original plugs I removed. The old plug electrodes are well beyond their useful life. All twelve had the same appearance, no fouling, same brownish grey color. I also checked all the plug wires for proper 2K ohm resistance plus checked them for leakage from center to ground as I have seen this before in the ML55 we own.

With everything back together the idle is slightly better but still not right. Revving the engine to 3-4k gave me a CEL. This time P0305 cylinder 5 misfire. It must be right at the threshold of fault range. Cleared the code and tried revving it again. No CEL this time but still has an obvious intermittent miss at idle.

Not sure where to go at this point.