Just realized I should update this thread with the eventual resolution... d'oh!
The underlying problem on this whole calibration run was, I believe, due to using an older version of cal.exe to do the first 3 steps (due to the "nan" problem with v1.0.2
viewtopic.php?f=32&t=814). Once I found and eliminated the one static log file which was causing the NAN issues, all the steps ran smoothly, with no need to set the variance manually, and MUCH lower MAEs (was in the tenths, now in the hundredths). This was not just a matter of changing the spelling of "ALN" to "ALGN," it seems like the whole set of data generated by the older cal.exe was just poor, or somehow incompatible with the newer sim3.exe.
The saga got continued in another thread, which is why I neglected to update this one.
viewtopic.php?f=35&t=807&start=10#p3981-Max