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
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.