I am no expert, But here is my advice. It looks like 12K is about right for an above average mile 54/05 model, I would go for a manual, as an out of warranty high mile DSG would worry me, and not all early DSGs have the paddle shift. And I wouldn't worry to much about getting the larger wheels, I would prefer a tidy set of 17s than a tatty set of 18s (the 18s only look better on the 3 door anyway, just my opinion) also some people say that the GTI is nicer to drive on the 17s.
Following my recent experience I would check the aircon works, and check all the electrics are ok. You should hear a pfff noise from the turbo when you change gear, but any whining noises are not good. The car should also pull away strongly in 3rd gear practically from idle with no hesitation.
One other thing, if you do get one use 98 RON Unleaded it does make a difference with these engines.
I am sure other people can add their advice.