Trying to fab a make-shift water-tight box defeats the purpose of the snorkle, and the "cold air" intake. The best thing to do would be go back to the stock box.
On a side note, after years of trying k&n products, I would get rid of that particular set up. It offers no increase in power, and no "cold air" benefits for the tacomas/4rnrs. Several people with deep pockets have even dyno'd different set ups, and because of the way these engines are tuned, it basically only increases intake noise.
In addition, k&n filters are horrible at actually filtering. I never had problems with the oil (which is just due to over oiling), but the whole inside of my intake and MAF was covered in dust, tripping the check engine light numerous times. The nice thing was, I knew the source---> k&n. I've gone back to the stock set up, and it feels more responsive than the deck plate hoax or the "cold air" jobby.
Caveat, if you never wheel or go off pavement, then the k&n will be fine. It cleans up the appearance of the engine compartment. However, if you could sell off the set up it would help off-set the cost of the snorkle.