Flashing CEL and the rough idle seem to indicate a misfire. I have seen coil paks fail on these. One way to verify it is the coil pak is to move that coil pak to another cylinder and see if misfire follows. Would be easier to do if you had your own scan tool, I found that VAG-Com is best. And have the cam tensioner seals ever been replaced, as they are also known to leak, the pass side one is at the rear of motor and will drip right onto the CAT. And I would personally stay away from any oil with a "zero" for the first number on these cars. They just make it easier to leak oil and the motors run warm oil temps anyway.