Maybe try a few strategically placed (but hidden) bowls of baking soda or vinegar near the box(es). Like, in a decorative bowl on a bookshelf or something. I know vinegar is good at countering cigarette smoke (don't know about it's effectiveness with cat pee smell, besides as a cleaning solution) and baking soda absorbs any smells.

I agree about Febreze. I can't stand that stuff.