The hole in the wall of the smuggler's box will be covered with a plastic cover plate in the same way I made one in picture #1. The hole in the floor of the smuggler's box will be plugged with a plastic cap or a rubber plug.
I actually have the missing socket for the air hoses in picture #2, so that takes care of that point of entry. Hole #3 can be covered up with a plastic PVC plumbing cap from your typical home improvement store.
http://forums.pelicanparts.com/porsche-911-technical-forum/423361-438-lbs-gone-5-days-my-build-story-4.html#post4117060