..
N0040 G53 G90 G40
N0050 F1
N0060 (Part: RE-7 upper bag mount)
N0070 (Process: Plasma, Outside Offset, 0, T1: Plasma, 0.0394 in kerf)
N0080 M06 T1 F85 (Plasma, 0.0394 in kerf)
N0090 G00 Z0.1100
..
N0130 G28.1 Z0.12
..
As far as I know, G53 needs to be on each line where it applies. On line N0040 there is no move, therefore it does nothing and is forgotten. On line N0090 it needs to be G53 G00 Z0.11 when you want absolute Z0.11. But line N00130 should go before it, to do referencing (i.e. seek and set home position), before you do any first move. In order move to known home in Z, would read N0130 G28 G53 Z0, for example, not G28.1.
line N0090 G0 Z0.11 could go to anywhere when the machine coords are not set. Additionally, N0081 G43 H1 is missing to apply tool offset coordinates. M6 doesn't do this. Missing G43 H1 too makes the Z move hazard. (Your post processor might not know about G43 Hn)