Trying to compair the two cars (Scooby 1999 year and S4 03 year) is tough as they really are two different cars.
What i would say is that the S4 actually feels slower, but isnt, the only thing i can put this down to is the ride and that its not turbo charged, where as the S4 has constant progresive power the scooby is sluggish up to around 3500 RPM then the turbo kicks in and you get a wollop of power. Also in the scooby you feel all the speed (rattles, wind etc etc) where as the S4 is so smooth you dont realise what speed you are doing.
I would say the S4 has more grip, but you dont feel like you can throw it around like the scooby - this may be just me still getting used to the S4 and the progressive power steering. Also the scooby is slightly smaller which helps you throw it around more.
Which of the two cars do i prefer - the S4 hands down, its just a far far far better car all round.
There are a few scooby owners where i live (not essex

) and have already had some fun with a few of them, beating them every time, even took a 911 yesterday - guessing i caught him off guard though.
Currently have a clean license but not sure how long that will last now
Prior to getting the S4 i was looking at buying a new scooby or a an A4 2.0 FSI Turbo S-Line - then mate got me a great deal on this S4. Wife drove it for first time yesterday and came back grinning, her quote was "im glad you didnt go for the new scooby now"
The down pipes, rear box and cats sound like a good idea - if only to get the full sound of the V8 - but that will have to wait a bit due to the cost.
Spike