Emissions issues aside I generally prefer the manual car to drive. In my Aero S3 the manual gearbox was pretty stiff when new and has just got better and better over its 13,000 miles. Having driven several S4 Aero autos, plus Aero Supersports auto, and a Plus 8 auto I always find the auto winds up too much, creeps too much and I can't get used to the +/- backwards/forwards since I'm used to the other way round. However, I'm also sure the auto is faster (the manual box has quite a slow change, especially 1st to 2nd) and if that was what you ordered that is what you should have got.
There can be some driveline noises with the manual box. You'll find a lot more information on the manual box under the Aero 8...
Whatever happens you should seek compensation, and on a personal note, really sorry you must be rather disappointed having waited for what is a truly wonderful car to drive...
