"The physical problems with recreating the accurate conditions would be nearly an impossibility."
Thats not accurate, the physical problems [i.e conditions] can be systematically simulated, there is more that we know than we don't. The recovery of the Hunley gives us the majority of the answers; we have the end product to the test to. All that has to be done is test logical scenarios to get the same answer. The navy recreates this problems all the time and attains good answers. The unknown can be attained by multiple test and getting an average. After WWII excess submarines were tested for just these answers to concussions and its possible damage to crew and vessel. Hundreds of test were performed. From these test came the designs of the modern submarines we know today.
Everything [that is known] about the Hunley's attack on the Housatonic can be tested and almost every other possibilty [that was possible] tested to the extent we can determine exactly what stresses the Hunley and its crew was exposed to. Knowing the limits of each test will give you answers of what did, could and did not happen. Once you understand the limits the "what ifs" can be much more easily answered. The first test will be always non-conclusive as parameters will be adjusted and recalibrated. The test on the glass ports gave some data to the puzzle, thats all. Keeping an open mind and being determined will solve the Hunleys' fate.