I am working on a 2000 clk430. Rough idle hot or cold and runns great otherwise. First suspected motor mounts and here is the test i did to eliminate this. If car runs with same roughness whether it's in drive or reverse i usually can eliminate the motor mounts as the problem. Poor motor mounts will generally give different rough idle in drive vs reverse. If the mounts are completly ruined you might not see a difference between drive/reverse but you should see the problem by prying on the engine and looking for collapsed mounts. For the trans mount do a visual and then pull down on the drive shaft to make sure there is still some flex.

If you suspect the exhaust system is causing the rough idle, jack up the exhaust a few inches (don't jack the car!), if vibration dissapers that is the problem. Also remove all the rubber exhaust mounts and see if vibration dissapears (don't drive the car in this condition, w/out the exhaust mounts).

This engine has 2 plugs per cylinder (a and b circuit). With a MB computer tool you can turn off the "a" plugs and see if the idle gets better or worse. then turn off the "b" plugs and observe. If there is a problem with only one ignition wire, plug or one side of a coil you may be able to see it because the imbalance is removed when you eliminate the faulty "a" or "b" ignition circuit. Furthermore with the computer tool you can see which cylinder is running poorest. Without the MB computer you must first take off all the "a" circuit ign wires and run the engine, then plug them back and take off all the "b" circuit ign wires. Just take them off from the coil side which is easy. What you may feel is the circuit that has the imbalance if the problem is exclusively in one of the two circuits. This is what i discovered, so I know my problem is ignition related and the "b" circuit in my case. The miss is not strong enough to trigger a check engine, but it is is noticeable.

The manual method i described above will trigger a check engine but it will go away after a few drive cycles or you can erase with a generic OBDII tool.

Don't forget to check for vacuum leaks, also try disconnecting the MAF and reconnecting (with the engine off), a poor contact/connection can alter the MAF signal by a few mV and fools the engine about air mass but may not trigger a CEL. A lean/rich code can also come from a compromised contact at the MAF connector. Many MAF sensors are condemned when in fact it's just the contact that gets "fixed" when you swap in a new one.
Good luck.

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1972 450SL
1982 300D Turbo