I'm not sure I understand what I read.
The rework was done, the dealer put the top box on the new mounting plate, you took it off at home and can't get it back on?
The recall kit is basically a metal plate that gets taped to the bottom of the box, a new plastic mounting plate, a rubber strip for the top box and a couple of plastic rivets. The metal plate should be flush on the bottom of the top box. If the plate is not flush it would be because the rubber feet weren't removed from the top box.
If the trunk and mounting plate were done per the recall and the dealer was able to get the top box to clip on but you can't it's time to call the dealer and ask for instructions. There shouldn't be anything different between mounting the pre and post recall trunk.