By placing a box over an open drain you are just slowing down the entrance of sewer gas into your home. Apparently the trap for the shower rough is dry. Either cap the waste line off properly or make sure you continully have water in the trap to seal the sewer gas in the pipe. The sewer smell may well be coming through your furnace ductwork. Especially if there is a return air opening in the basement in the vacinity of the roughed bathroom.