Lately I've noticed that whenever the engine's been shut off for more than a few hours, when starting it's running rough for between 2-8 seconds, then resumes idling smoothly. By rough I mean it almost sounds like it's running on 3 cylinders, interrupted-like. It tends to do it longer (around 8 seconds) when started in the mornings.

I scanned the car some weeks ago and there were some misfires on cyl 2, switch the no 2 and 3 coils and the misfires went away. Then they appeared on cyl 4. However, the car idles fine after the initial hiccups (by fine I mean there's still a movement of the needle every now and then, but I've given up on fixing that one).

I didn't scan the car at cold startups to see misfires, the ones mentioned above were with engine warm. One question though: looking at vag-com block 14 and 15 (or 15 and 16, the misfire blocks), the counter went up and then reset to 0, then up again, then 0 again. Shouldn't the counter be logged somewhere? I mean, I saw these misfires by accident, because no codes were logged.

may be your secondary Air Pump thingy, common problem. some run OK when it blows a bit,others run like poo. search for "secondary air pump fix" and you will find loads about it. If you have iffy coil packs better to get them changed or at least get one as a spare ready for when one dies as it is not good to run the car with one down, causes damage to the CAT? IIRC?