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Been trying to get the estop and machine on circuits working properly today with help from marks mh400e information which he kindly sent to me. 
just wondering if the older mahos have the same estop chains and components?
 

Thank you so much for pointing me in the right direction. 

Yes, any AI I asked eventually started hallucinating code that broke things. 

I did have someone send me a template HAL & INI set for the machine I am using (a Platform CNC with upgraded linear rails. Excellent hardware, currently being let down by confusing software, and its operator.) I was able to cobble something together that mostly worked, after much iteration. Since this was done manually, it didn't help me with learning and using PnCConf, which I would prefer. 

At this point I have everything moving, but until I sort out homing, the Y & Y2 axes are not moving in unison. They are seen as separate Joints 1 & 2. I assumed there would be some way to simply lock them together as one gantry joint(?), but apparently that's not how LinuxCNC works.