While Looking for some ideas to minimize the printing and manual crafting time per-unit, my Fiance found the answer in the PlumbQqik PQC-104, a flexible end cap for sewers and drains. It turned out to be only a few millimeters off in both height and diameter from the existing case design. I adapted the existing top and center bracket to a new design that clips into drain cap.
While it will add significant cost (an additional $5 per unit), it shortens the 3D printing time down from three 2-4 hour parts to a single 3-hour part. I also no longer need to tap screw stalks and there is far less support material to remove. Additionally, it solves the problem of the visible layer strata, which would have required some sanding or better tuning and leveling of my printer.
I've also settled on using the vinyl cutter to score patterns for the edge-lit acrylic. I still need to get better at scoring and snapping the sheets down to the right size, but the results are looking nice so far, ignoring the rough and broken edges.