Kent,

b. If I override the warning and continue anyway, I get a different
popup stop window with the message "Linear movement on line 20 would
exceed joint 2's positive limit / Position relative actual".

I had the same problem. The issue was caused by the axis soft limits, which
are set in the machine.ini configuration file. In my case, using stepconf, I
seemed to end up with the Z axis having a default envelope from 0.010 to
-4.000. I was having problems changing them in stepconf (I had multiple
values get set to their defaults rather than my entries, not sure if there
is some bugginess there) so I just edited the ini file and things worked
fine.
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