Before you tune your VW, it is important to understand some important maintenance items for direct injected engines.
#1. Spark Plugs: Direct injected engines can very sensitive to spark plug wear. Even though your car ran perfectly stock on your high milage plugs, when we increase cylinder pressure with more boost or timing, they will likely be a source of misfires or "knock". Check your manufacturer recommended spark plug replacement interval, and if you have any doubts about their age, go ahead and replace them with OEM replacement plugs from your local dealership.
#2. Coil Packs: Many German engineered direct injected engines have a propensity for coil-pack failure. If you are throwing a trouble code for a specific cylinder, you can troubleshoot the issue by removing your engine cover and swapping coil packs with an adjacent cylinder. If the misfire follows that coil-pack to the cylinder you installed it to, that specific coil-pack is likely to be faulty. These should be replaced with OEM replacement coil-packs from your local dealership.
#3. Carbon Buildup: One downfall of direct injected engines is buildup of carbon on the back side of the intake valves. This was prevented in older port injected cars (1.8T for instance) by fuel washing over the back of the vales. Being that your fuel is being injected directly into the combustion chamber, and never touching your intake valves, soot from your EGR system or oil from your PCV system can cause buildup. This carbon buildup can cause misfires or poor running/idling. If it has been more than 40-50k miles without a de-carbon, it is wise to go ahead and have that done. Yourself, or a quality mechanic can check your valves using a bore-scope if you are uncertain.