The goal of the XYZ stage is to be able to position the STM tip quickly and to enable relatively course scans of the surface topography (for example to choose an area to gather atomic resolution data interactively).
As I turned the stage micrometers I noticed that there was a small amount of static friction that would cause the micrometer to bind when trying to make very small changes to the position. I removed 1 of the 2 springs from both the X and Y stage and was able to eliminate the vast majority of the binding.
I also started to model the stage in CAD so that I can design the motor mounts