Great project and it looks great as well.
I'd start by trying to measure the register distance. Put the camera on something flat, remove the lens and measure from the lens seat to the film. Measure at several points around the circumference and compare to what a Mamiya Press should have. My experience with 3D print is that it isn't very precise not very flat/perpendicular.
First correct that and then use some paint/coating/flocking at the inside to make it lightproof.