Can't believe this happened, and just highlights the importance of getting water ingress issues sorted asap for other members. So who footed the bill?
Was it your insurance company or Audi?
Bose would be easier to retrofit but I'd recommend you speak to autologics or Audi retrofits as members have used them for retrofits and been happy with the results.
I'd recommend a diagnostic check to see if any fault codes flag up. As it could be an issue with the mad sensor, lambda sensor, cam sensor. What's the oil consumption like?