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I still have a weird issue that I am thinking is my hardware somehow, I can connect in the test GUI, see inputs, quadrature encoders and toggle outputs, but the terminal window keeps saying received data have wrong header. I have triple checked pins for conflicts. Apart from the terminal spamming that message it seems to test OK. 
Unfortunately LinuxCNC won't get out of estop, and spams wrong header size.

I am still treating it as my hardware, going to setup a different PC, I took out the Tang Nano that is in my milling machine and flashed it but the fault persists. If not the PC, I'll start swapping out PCB's from my two working machines.

Worst part is it was all working nicely last night.

Update,

I have successfully added the emergency stop button. The problem was with the Mesa 7i95 board's nomenclature used for input/output pins. I was using the wrong pin (hm2_7i95.0.gpio.000.in). The correct input 00 pin for the Mesa 7i95 board is inmux 00 pin (hm2_7i95.0.inmux.00.input-00). Below is the code added to the hal file...

net estop-out iocontrol.0.user-enable-in
net external-estop-in hm2_7i95.0.inmux.00.input-00 => iocontrol.0.emc-enable-in


The next problem is still pending about the feed override.
Thank you, Benb and PCW, for your input. You are correct that I want to control feed override using external analog voltage control (cRIO-9045, NI-9775, LabVIEW Software). I have never modified the Mesa default pin configuration, and I am trying to search for how to modify the Mesa board pin configuration. It would be great if I could use the motor or encoder pin for analog input. I request that you give me more ideas/references to do the same. As PCW suggests,  "The 7I95/7I95T has no analog input, so an encoder is probably a better choice." Kindly give more hints on how to use the encoder to control the feed override using external analog voltage control (cRIO-9045, NI-9775, LabVIEW Software)

Another idea I am thinking about is serial communication using the serial port available in the Mesa board; there are two serial communication ports (serial 1, serial 2). But at the moment no idea how to do this as well.

Another thing I was trying to identify was the pin/parameter that is responsible for feed override. In Axis GUI, there is a button for feed override, but I am not able to locate the corresponding pin and parameter in the Halshow Configuration window. I do locate one pin, but it is saying it is not writable. A screenshot is attached.

Thanks

was my mistake, normally I give a warning/error if a pin is used twice, but I had once installed that you can use input pins more than once and forgot to check if both pins are marked as input.

is fixed in dev branch

Hallo ich habe den Test an 2 Verschiedenen Mesa ausgeführt