It is not so easy to see how the z-axis moves as it is all inside the microscope, and I have not looked at the range of travel. I am not able to get to the lab for a while now, but I would suggest printing the separate z-axis that is for the upright and operating manually. Then you can move faster and see more inside and check what is hitting where.
One thing that has just occurred to me is stringing inside the z-axis. The roof above the z-axis in v7.0.0beta1 has unsupported bridges. Depending how that printed, it might leave strands that block motion in one direction. Is the motion equal up and down from the nominal neutral position? neutral is as printed with the base of the z-axis optics mount level with the base of the microscope. I thought this was just a cosmetic problem, it has been addressed anyway in Z axis printability enhancements (!335) ยท GitLab. The current master build has the changes incorporated (thread Openflexure current build is here! - Announcements - OpenFlexure Forum)