IIRC the supercharged engine was a 2.8, what Docs car originally was before a 1.8t conversion, quite a rare supercharger kit too.
Not quite right that was my first A4 a 97 2.8 30v which I bought a new PES Supercharger kit for and was a great car but a 1.8T offers more and when a 1.8TQ came up for the right price just before I was ready to do the conversion and bought it and the rest is history.
Ok back to the swap.
The back door need the whole window frame which contains the whole contents of the doors on one frame held in place by 4 bolts and shims as the RS4 Avant as diffrent window frames to a saloon/Sedan.
The front doors from your S4 can be used but you will need to de-trim the outside and grind of the pins and make good.
Front wings will just bolt on but you will need new wheel liners as the S4 ones will no longer fit the larger arches the front bumper will need the bumper shocks as they are longer but you could get round this by using washers.
The rear quarter will also need the inner wing not unless you body shop can either fab something up or even fiberglass the void fron the S4 inner wing to the RS4 outer wing/fenders.
The rear bumper (if using your current bumper) will need to be heated on the side and teased out to follow the RS4 wing/fender shape but I would buy a Euro S4 rear bumper and do the same to that using a heat gun and your knee making sure you don't over heat it.
Bonnt/hood are the same and so are the lights so nothing need hear but the front wing indicators are different shape to standard so you will need to replace them, I think they are TT units/B6 A4 units.
Engine sump gard is different and the S4 unit will no longer fit so either leave it off like I did or a RS4 unit will cost £200/$360 to get the correct one.
Petrol flap will also be needed to flow with the RS4 rear arch profile,
Side sills/Skirts are stuck on with double sided tape as is on the originl and one or two screws either end in the inner wing/fender. You will also need to bond it to the under side as the mounting point under the car are different and you wont be able to secure it in the same way as the RS4 plus you will have no reason to remove it.
This should cover most of the conversion and the pictures will do the rest.