Using the 100mm lens on an APS-C instead of FF camera will increase the distance between the negative and the camera, also increasing the want for a giraffe neck 
a flippy screen can help though.
I’ve taken shots with the gear you mention, but with an EOS M6 instead of a Fuji. Both combinations work well on a copy stand type of setup. You could get an alternative setup using a black round table leg from a hardware store and a clamp like so instead. Use mirror lockup or live-view and the self-timer to reduce vibrations.