Hi Mursal. Well, yes it runs very smooth after a minute or so. However, if I'm stopped at the lights or whatever, it seems to be shaking a little more than it should be, but it seems to be running smoother since the coil and then smoother again since the leads were changed, but it still misfires on start up, every start up(hot and cold) and the engine flight flashes for 20 to 30 seconds as soon as I start to drive, or even if I leave it idling. And while I mention idling, it doesn't always idle in a stable manner. It seems to rev in neutral by itself when I'm at the lights. Not much but a little bit. But I did change the thermostat and Coolant Temperature Sensor very recently which had been acting up previously.
I haven't run it in VAGcom yet but I might invest in one from ebay and run it through.
It's sounding more and more like a cylinder problem to me though. Symptoms are similar(not identical) to a friend of mine who has a 05 polo and he got occasional flashing engine light, at all different times during driving but not very often, and it eventually turned out to be a cylinder. He eventually lost a second cylinder before finally diagnosing and had to have them rebuilt into the engine(or something like that). Mad stuff.