That's a pretty good challenge, sir!
As for the character animations, there's no problem at all: I'd create a sitting posture and then a gesture for the cranking cycle, so it might be easily merged with other possible gestures.
But first things first: and what's needed to start working on this project is creating a model of the interior of the Hunley's cabin... which poses the real challenge. And it's so because as of this date there seems to be no such thing as an official and historically accurate reconstruction of the internal arrangement of the Hunley. For example, in the idealized reconstruction shown in the first image, just like in many other images out there, the crew consisted of the commander and eight men serving the crank; on the other hand, according to other interpretations, there were only seven men at the crank, apart from the commander, and, in fact, that would have been the composition of the crew in her last mission. Also there are discrepancies about the commander's post: many images depicts the commander standing while steering the ship and glancing out through the little windows on her forward port; others say the commander was actually sitting.
Anyway, I think this would be an exciting project to work on, and a movie able to convey the oppressive claustrophobic atmosphere inside the Hunley in her last ill-fated mission, would be a pretty damn good achievement and a modest homage to the Lt. G.E. Dixon and the brave men in his crew.