I reversed the Y axis connections and tweaked the software some more.
This picture demonstrates that one remaining issue is related to the Z Axis. First 5 characters on first line are supposed to be starburst, space, A, Z, 0 and 9.
Seems like hooking the Z axis to my scope with a 10x scope probe causes a lot of latency in Z axis display, due to RC delay in the Z. The lag causes a line to be displayed, to actually not show, but the next line will show. Changing the probe to 1X causes Z axis to completely not function. Could be my Tektronix 465 isn’t compatible with the SCELBI design. I’ll have to investigate both the scope and the SCELBI O-scope implementation in order to find a good fix.