Car Audio: Would it sound much better if I replaced the factory Audi Head unit with a aftermarket deck ?

No it would not. A lot of people do not realize that MOST factory head units are better quality in sound quality than an after market one. The noise you are hearing is most likely ground loop noise. You prob do not have a good ground on your amp. Or it could link back to your LOC (line output converter), you prob used one because it is a factory head and will not have RCA outputs. If you wired this up wrong it can be your problem. Also do not run your power wire and RCS's on the same side of the car. You did not give me much info so this is the best help i can really give with the info provided. Hope I helped.