You may have mixed up the wires to the plugs: i.e. #4 is now on #3 spark plug, for instance, easy to do on this engine, especially when changing wires.
The other possibility is a bad coil unit. Some shops change the three coils as a matter of course, about $12 each on the internet.
If it wasn't rough before then you need to review everything that was done; there's a mistake; it's not due to the spark plugs - unless they are incorrect for this engine.
I recently had a similar adventure with my '97 E320 (straight six). First thing #2 coil's hold down screw broke and had to be removed with an Eazyout, then a new Champion plug slightly misfired when cold so I removed them and checked their gaps, .032" OK, bought new seals, put it back together and it still misfired somewhat when cold. Then I installed the Bosch platinum +2 and it now runs perfectly.