Option A: With demand for 981 cars being strong, even the base models, I think you can recoup your losses by selling the car after replacing the box. In fact, most used car buyers would like to have a new box anyway.
Option B: However, if you keep the car, you will basically have a car that has already had its biggest ticket item sorted out. The other known 981 issues, of delamination on the headlights and the warping of the door panels, are more cosmetic issues. But, those are still expensive issues (one of the door panels is R25k to replace).
I would lean towards Option A. Get the new box and sell the car, only if you can get an offer that makes it worthwhile. I feel the 981 will maintain its value, so take your time.