[flimsypremise]

I'm currently doing something similar to build a photographic film scanner. I will say that I've found that moving the optics is generally much more error and vibration prone than moving the target. I'm actually using a 2 axis microscope stage as the basis for my scanner, ironically enough, and CNC spindle z-axis for focus.

[anfractuosity]

Cool, that sounds really interesting, what size film are you using that for? Is illuminating the film evenly hard too?

[flimsypremise]

I'm shooting to do 35mm and medium format. 4x5 is a stretch goal. Even illumination is definitely a challenge, though I use the same technique you do, which is generally refered to as flat field calibration, where we capture the field of light without any target and use it to calculate the offset to apply an even field. One of the trickier aspects is finding affordable lenses with appropriate magnifications that can focus evenly out to the edges of the frame. There are various lenses pulling from scanners or that were specifically used for copying that are useful if you can find them.