This gives me flashbacks of when I did all this stuff too. My brake lines were just like yours - destroyed. Those were kinda of a pain haha.
I'm so jealous you picked up that A6. How many miles are on it? And how much was the car, if you don't mind me asking? I've been looking for a good parts car for a while now, and they all seem to have 175k+ miles, or are nice, running and driving $3k+ cars.
Also, I believe you can use an S4 subframe as well. I just swapped my front subframe and did a whole bunch of research, and apparently, all B5 subframes are the same (despite small revisions that don't affect mounting points) except for the manual 1.8t. I used an S4 subframe and it accepted the 2.8 trans mount/bracket perfectly fine.