HI i have a merc C230 SLK R-REG which has a misfiring problem.It idles rough and when i try to accelerate it misfires and at times pops back.I have just fiitted this replacement engine since the original one had a small end knock at times it responds ok when cold then starts to misfire a few minutes later.The other thing is the hard top convertable roof has stopped working ,when i push the button forward i can hear the motors but in the opposite direction the button flashes and nothing happens.Is this because i had the battery disconnected for a long time.I would appreciate your help thank you.

I'm getting the same thing on M111 2002 C230 Coupe.

From reading the C class service DVD I know that the ECU uses a ratio calculation of number of misfires out of good fires.
As such, I've only had it throw a CEL once recently, since it apparently didn't
misfire enough to meet the criteria for a CEL.

But you can feel it, but now only at WOT! And yes, I get the misfire and sputtering. My car is fairly customized which I'm certain won't make things any easier.

The problem started when the Cat. crapped out.
The symptom for that was, misfires but always with a CEL and only in the high rpm's. I was able to diagnose the issue myself, thankfully, once I determined it was not a Coil pack. On top of the hi rpm clue, I actually had grey powder around the outlet of the exhaust pipe.

(BTW, are you getting any CEL's? Is is a particular cylinder? Swap the coil pack with another cylinder, and see if the problem stays or moves with the coil pack.)
I got a Magnaflow Cat. as I don't have 1500 for a Mercedes one.
It's supposed to be high flow.

The O2 sensors have never been replaced and I'm at 113K miles.
I know that faulty 02 sensors can cause the fuel system to dump more fuel,
but how do I know if they are bad?
My OBDII reader gives voltages on them, but I don't know whats considered good voltages.

I'm thinking of picking up an ELM323 interface, so I can log the results as I drive on my PC and see which cylinders are misfiring!
When it misfires, it stutters, but so far only the one CEL.

Any ideas?
I'm thinking it could be anything from a faulty spark plug, to fuel issues
(but the filter's been replaced)
Any troubleshooting suggestions on this anyone?