I like Tenchu's idea of the "sealed" box gimmick. I already though of a lot of possibilities a few minutes after reading that, so thanks. Cool idea Tenchu.
As for Pulling Through, if you want to make it stronger then the things that I think would make it so would be to able to let the spectator hold on to something (card or box) during the penetration, or maybe you can create the illusion of the card already halfway through the box by showing the box sideways. I haven't really got into thinking of how to do these but I think they'd make your effect stronger.
EDIT: I was thinking of how to do the things I said above and I think I came up with a little foundation you can build on.
Please tell me if i'm saying too much, I'll edit this if so.
If the back of the box is the same as the backs of the cards, like Bikes, then you can easily show the illusion of a plain box with the deck inside, even when looked at from the back. The specs won't notice anything. You can even let them hold the box, the texture of the card and the box isn't very noticeable if you get the spec's attention to something else or if they're holding it with only their thumb with the 4 fingers on the front of the box. I guess this will cover the inspection prior to the penetration and the only other thing you need to take care of is the half-moon cut at the back of the box. Maybe you could just cover it with your hand.
If you want to let them hold onto the box during the penetration then, I think you should first melt the card halfway through, then let them hold onto one end of the box, the end that you're pulling away from. That way you can melt the rest of the card through while they're holding the other end of the box.
If you want to show the card halfway through with the box sideways, I thought of showing the box sideways but use your hand to partially cover the end of the box that you're pulling away from. From there, place you forefinger parallel to the card and the end of the box then use it to bend the card against the part of the box where it's hanging from. It will look like the card is coming out from the middle of the box. Use the thumb if necesarry to make the card straight while you're bending it. I though of these with what I think was your method in mind, so I may be wrong. If it's right, then you'll get it. These are the best I could think of right now, so maybe you could make it better.
Hope this helps.