I know that replacing both the gear cables resulted in me stripping the interior as you have done. I did it as a precaution.The car had done about 55K miles at that stage (it has now done 65K miles, 12 years later).
Frankly, I would replace ALL the rubber hoses whilst you are at (budget permitting) including the valve and heater matrix (only if you can buy new).
In my experience, cars (in fact all manufactured items) are designed to be built quickly and cheaply, not taken to bits. Audi is the same.
It is a job that I never want to do again. Best of luck.