I am using a gantry style CNC with an 8' gantry. I use the PMDX motion controller and Mach 4. It is simple to set up the slave axis in Mach 4. My motors turn in the opposite directions on the slave and this was simple to assign. Also, once you slave a motor in Mach 4 it will force you to keep the velocity and acceleration for both master and slave the same. Not that I have ever tried to set the master and slave to different values and seen the Mach 4 error box
It is very easy on Mach 4.
Also, I am no Lua coder, however, I have been able to add lots of buttons and Lua scripts. I tend to find something close to what I want to do and just copy it.
There is a lot of new stuff being made for Mach 4.
I am not sure if this would work for you, but perhaps you could have a different folder with Mach 4 for each configuration of the machine you would want to use. I know you can have multiple copies of Mach4 in different folders. You could have an icon on your desktop for each configuration of your machine. Mach 4 will not let you run two configurations at the same time so it would avoid conflicts or race conditions. I would do something like make the background of the screen a different color so there would be no doubt about what version of the machine the operator was running.
This would seem to be a much easier way to approach the machine you are talking about, however, I am sure the pros on this board can offer a better option.