You only need the radio removal tools, they slide in place and you will hear a click, then pull the radio out.
http://cgi.ebay.co.uk/Genuine-Audi-...arts_Vehicles_CarParts_SM?hash=item1e5a7c00c4
Have you checked your booklets, usually service book has the code if its been printed!
You shouldn't have to put your code in again as that unit should be coded to your car.
Stock HU is fine, just snip the Bose EQ wire on the back and regain all the highs and lows that Bose deny you. Run the amp for the sub off the rear pre-outs and the fronts off the HU or go with a 4channel amp and run the fronts from the other 2 channels.
The amp fits in the other side, here's the original Alpine I installed and then upgraded to a Genisys, far warmer and more musical:
I wouldn't bother with the rears. Concentrate on the fronts and the sub. Here's my stealth sub fitted to our Avant:
Yes, so did mine. You just remove the rear panel and cut out the back of the cubbyhole. You can do this really neatly so that if you wanna go back to stock you can easily hotglue it back in place.
I made the enclosure and the sub is a JL Audio 6.5" sub (as I use them in my A3 stealth subs) but you could easily fit the 8" version as per this B5 Avant I did last year: