what plugs and leads are you using?
Good question there.
And what Khare had done to check your arm and cap? Are they in good condition?
If you can, get VAG-COM setup and check the status' of the major bits and when the fault occurs read off whats going on.
Example would be Measuring Block 003 which gives the Throttle Position. Mine used to go up from 0 degrees to 13, back to 0 then start again at 18 up till 72. Faulty and a new one from VW was £96. Can try unplugging the TPS to see if it makes a difference. Would depend though on how harsh is your misfire? Does it feel severe like one cylinder is down or like a mild stutter?
My alternator was overcharging causing a mild stutter misfire type fault from just above idle speed to 4k rpm, your description of the fault sounds quite similar to what I experienced - Check the voltage of the alternator with a Voltmeter but ideally with VAG-COM when driving.
Also check your Vac pipes aren't kinked or knackered especially the one to the fuel pressure reg and to the ECU.
Try that and let us know how you get on