Hi Vishal, sorry to hear your 10k loss in shootng arrow in dark. Check engine light is always a mysterious issue if person doesnt have appropriate VAG diagnostic tool.
I can also suggest 5 more things to check or change, as per my knowledge but the best is find good garage who have OBD II compliant VAG tool and run on your car to find the exact fault code and then see which item is pointed by those fault code.
More likely it seems Air flow sensor or some other electrical related issue that only fails 3 cylinders, quite weird.