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Like I said, you are doing important work :)
I'm just spitballing here, so feel free to ignore me. One of the ways to view and digitize slides is a lightbox like this. Would it maybe be easier to set up a camera and tripod similar to the way you would for copy photography, take a photo of each frame, and then use a script like this one to create a "slideshow" of the resulting images? The slideshow would be at 16fps, or whatever the correct rate would be. The camera would also naturally order the images as the filename increments.
You'd have to manually advance each frame, but you wouldn't need to manually order and compile a video. Maybe more work up front, but easier once you are on a computer.