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Right, swapped the coil packs from cylinder 1 and 2, cleared the code and now got a new code of p0301, so misfire on cylinder 1, suggesting it is a coil pack issue.
Checked the coil pack part numbers, looks like they are subject to the recall so I'll give the local skoda garage a shout tomorrow and see if I can get them to swap them out.
TurtleRecall
mi7rennie
Take the coil pack and swap it to a different cylinder, reset the code and take it for a drive, if the fault moves with the coil then it's at fault. If this is the same as the 8L S3 engine then there coil packs should be replace with newer items from a golf Gti. The uprated ones are red coils I think.