It looks like the density problems might be from the film itself? If you look at the second or perhaps 3rd row(it hard for me to see as im on my phone) it is lighter than the rest (maybe one or two more rows near the bottom also exhibit this). Maybe those rows were a bit thicker in density than others. Maybe copy them with a camera frame by frame again, or make some type of holder to do two contact prints.

As for registration maybe a simple setup of finishing nails evenly spaced on a board about 5.5 or 6 feet apart to latch onto sprocket holes at either end may help you line it up easier. You could slide your papers under and place a large plexi piece over it.

Very cool and very impressive by the way!

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