For the z-axis motor the new image is very clear indeed. Was the binding of the motor body to the red gear, or was it the flange of the small yellow gear binding on the large red gear? There does seem to be a little more of the brass shaft showing below the gear than there might usually be.
I also see that you have the released version 7.0.0-Beta1 of the upright illumination. You will probably have had trouble getting the mounting nut in. There is an improved version in development, noted on Openflexure Microscope V7.0.0-beta1 released - Announcements - OpenFlexure Forum