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Here is an update.  I have plugged the positive from my EDM power supply into pin 13 TB2 and the negative into pin 14 TB2 on the Mesa. I then evaluated pin hm2_7i96s.0.periodm.00.duty_cycle using hal meter. The number is jumping around like crazy. It got a little better when I remembered to change the jumpers to TTL. Now it fluctuates only on the low end.  

I have tried shielded cable. I have tried a RC filter with a .1 uF capacitor and a 3.3 kOhm resistor.  I tried switching the red and black cables around.  I tried tying the black to ground.  The signal becomes 0 if either the red or black wire is removed from the mesa pin 13,14.  But I cannot get a signal that makes sense.  The signal jumps around even when the EDM supply is turned off and remains unchanged even when the EDM is cutting. 

I currently think that maybe the problem lies in the sampling rate.  Or perhaps it has something to do with the pin.  I think the issue is in the Linux side but I could be wrong.  I will try using the oscilloscope more tomorrow.  

If anyone has ideas please let me know.

Best,
-Dylan

Yeah well the internet is full of information that isn't quite correct. Or sometimes information doesn't get updated as quick as it should.

So you have 2 options, argue the toss or use balena etcher.

Hi Thomas,
For the block diagram conversion to Hal netlisting  I use Eagle2hal its documentated in lthe inuxcnc wiki (old but works for me). However if I had to start again I would learn Ed Nisley's Kicad to HAL the source code is in Python  also the Kicad people are planning to release a schematic API in their next release this would make it easy to make run time changes to the schematic capture and animate the schematic with realtime values.

gist.github.com/ednisley/cd69ad5a899226067d7a4a92c2114568