hmm... i didn't notice the mix_limit = 5. I'll change that. That being said, that is for the joint 3, where the Z axis has a max limit of 0.001. i'm a little confused what the difference between these two values are, but it seems like it soft limits it at the 0.001 value, as far as i can tell my manually jogging and the machine stopping at a height of 0.001.
as for the the G53Z4.9 move, that would try to hit the limit switch. Are you getting that from line 31 in thepsng_manual_change.ngc file? like this line?
G53 G0 Z[#<_ini[AXIS_Z]MAX_LIMIT>+#<_ini[PROBE_SCREEN]Z_SAFE_TRAVEL_OFFSET>]
I thought this would evaluate to G53 Z-0.099, since my Axis Z max limit is .001
all that being said, i'm still very new to all of this so I probably don't understand things correctly all the time (well, no probably about it, i don't understand things correctly all the time