I see you mentioned using a 3D printer for scanning medium format film. I did something similar, but took the opposite approach. I placed the film on a lightbox and mounted that to the printer, then had that move around in front of a camera with macro lens. I did not have much of a problem with alignment.
That being said, this was a one-off, but once I had enough overlap with each capture, PTGui was able to switch it together relatively hands-free, even with it having lots of sky.
That being said, this was a one-off, but once I had enough overlap with each capture, PTGui was able to switch it together relatively hands-free, even with it having lots of sky.