Aluminum may corrode through from acids in the exhaust gasses. I don't know for sure, but I would not count on it holding up better than steel. If you make it out of good steel, it will last a long long time.
I have thought of using the box idea too. What about making it narrower - forward and back - instead of 6", and making your stacks either rectangular or oval near the base. The idea of this is it would take up less space in your box.
Blake