Q: cylinder 3 and 4 misfire

It all started with overheating, then we discovered the cat behind the turbo on the drivers side is blocked. We solved that, it wasn't still working well then I opened it to check for timming issues and I noticed the passenger side bank exuast and intake was off a bit, I then set it back cos am also a mechanic. From time to time I do hear the cam adjusters hitting the cylinder head covers but didn't want to think it could be the cause. Now it's worse, the engine is no longer working fine and cylinder 3 and 4 are not firing at all, even swapped the ignition coils but still the same. Now am guessing the igniters on the air box or cam adjusters making the engine timing shift. Secondly, if the notch and arrow pointing the direction of timing on the cams are slightly off, can it cause a big drop in power to the extent of not firing plugs 3 and 4. Thank you, Martin. My email -martospliff@gmail.com, Audi 2.7t 2000 model year