Hi mate, welcome aboard.
I'm not too up on the mk6, but assuming most parts overlap from the mk5, there's plenty of choice out there and plenty of good quality kit.
On my mk5 I've got a Helix Organic uprated clutch that works with the oem flywheel. I got the clutch along with a new flywheel from Alex at AKS Tuning at a very good price. The clutch is good for 400lb/ft, and apart from a heavier pedal, feels and acts like stock.
Revo intakes are probably the most desirable on the mk5. Great gains and flow. Also look at Evoms and ITG Maxogen.
Intercooler-wise, S3/mk6 R is a good choice and not too costly. If you have the budget something like a Peron would be even better. Bear in mind that some consider the bigger coolers like Peron as overkill on a k03 car (too big to avoid lag) but ideal for a k04 car. I'm not sure where the IHI turbo on the mk6 sits in that regard; it might be a good idea to speak to Alex, or Niki at R-Tech, and also have in mind your target for power in the future.
Stage 2 map, well I can only really recommend R-Tech, they do full custom mapping on the dyno and consistently create some of the best maps this forum has seen. I know they're now well into mk6 mapping, so you'll be in good hands. The more generic options would be Revo, GIAC, APR, and Shark Performance are very good. Unicorn do custom maps, and they're also very well regarded.
Alloys, they're a personal thing, but if I had a mk6 I'd be looking at BBS CH-R.
Hope that helps!
