I swapped them around again, and now everything seems to be functioning correctly (previous swaps did not resolve the issue). I think the main issue was the wire sequence for the motors that seemed to have mainly been my issue. I am not sure why the one driver would have a high vref though, but it hasn’t appeared again after some more testing.
I did adjust the firmware for full step (removed the 0 ohm resisters to set it to 1/8 step). With the default settings in the firmware (for 1/8 step) and running full step caused some interesting results. The Elevation seemed to work correctly regardless. The Azimuth though had some interesting homing issues. The movement seemed normal, but when it hit to limit switch the motor ramped up (stalling), and started winding down (causing it to rotate a little). It would then high speed move back over shooting the home switch and setting 0 not at the limit switch. Switching the firmware to be full step resolved that issue.
I used the settings mentioned in A new version of 5.18 geared nema rotator - #3 by iz5rzr for the full step (which is speed 300 step/s, acceleration 100 step/s^2, and SPR 200L, I also set the microstep to 1 even though I don’t think it is used in the firmware). This corrected the Azimuth homing issue.
Sometimes I just need to post about the issue and I soon find the solution, or information provided helps resolve the issue. Like I mentioned, a set of steppers that had just arrived yesterday really help figure out the main issue with the wiring. I had planned to use the new steppers, but the holding torque is a little low (listed as 76 oz.in) compared to the ones already installed from STEPPERONLINE (which is listed as 92 oz.in). This was interesting as the newer ones are sold by OpenBuild which have builds for DIY CNC machines.