Maybe I'm going a bit daft. Comments on the following welcome.
I have my 6040 CNC mill set up as standard, where the X axis is on the shorter side and the Y axis on the longer side.
Now it strikes me that as I access the machine from the side (and not the end), it would be more sensible to have the X axis running left to right and the Y axis up and down. If I laid a sheet of graph paper in front of me that's the way the data would be arranged.
It seems to me that this can very easily be accomplished by swapping the X and Y stepper feeds. And the appropriate settings for limit switches can be switched within Mach3.
Does this seem realistic?