Shifters for sure are different, you will need an 85-87 shifter & floor plate... '88 will work too if you modify the floor plate
Driveshaft(s) are different lengths
You probably will want a very early A4LD... like '85-87 IIRC... to keep the electrical part fairly simple
Also you need the kickdown rod, I believe it is different than the one you have on your C5.
Too bad you're not closer, I have everything you need for the swap minus the driveshaft! If you can find a transmission locally, I can send you a box with the shifter and all that stuff - yours free if you pay shipping. Personally I like the C5 better and would rebuild what you have but that is just my preference, I think it is a much stouter transmission.