Again I doubt that such a recreation will ever be done.
The physical problems with recreating the accurate conditions would be nearly an impossibility. For example just how would you determined just how hard that the Hunley struck the Houstonic with that spar? How much force would be applied to a spar to bend it? What is the maximum speed that could have been attained by seven men turning a crank powered submarine in those waters? And would the speed be high enough to obtain the amount of force needed to bend such a spar If you could recreate a spar equal to the period?
One of the Childrens exhibits at the center is a simulation demonstrating the resistance of water acting against such a propulsion system. You get inside a hull and turn the crank attached to a reproduction of the propeller which is inside a tank of water. It is not an easy thing to do to build up any speed and demonstrates one of the needs for so many men to be inside the vessel to act as an engine. How would you determine what the physical strength of each of those men would be to determine what kind of physical output each would be able to produce?
My point here is that even in your most "accurate" recreations there would be undeterminable elements which would have to be assumed, that would still lead to the same spectulations by critics that we have today. So you will have accomplished nothing at great expence.