I think keeping the IBU's the would be good. It should give you a good comparison of the flavor each hop variety adds to the beer. However, IMO I think you might want to get a scale and adjust the amount you add to the boil. I think it would be difficult to control IBU purely by boil time, particularly if you are trying to compare something like a13% AA hop to a 3% AA hop. But it is a cool experiment.
I'm not crazy. My mother had me tested.