Divide, Conquer, Guillotine, and Requeen.
Divide- break apart the hive and move the brood 25 to 50 feet away from where the hive was Leave a honey supper on the original bottom board.
Conquer- this greatly reduces the population that you are dealing with at one time. the guard bees go back to guarding at the original hive location, the foragers are returning to the original hive location as well as bees that fly out of the hive. Now with 2 or 3 manageable bee populations finding the queen is much easier, In a few minutes you should be able to hear the difference between the super with the queen in it.
Guillotine, and Requeen- now that the task of finding the queen has been made easier and a less daunting and intimidating process. KILL HER and requeen.
Be prepared, Have your new queen ready to install, by the time you have the colony queen less and put back together It will know that it is queenless so the new queen in her cage can be placed in the hive.