Novakon Mill Conversion - Getting Started

So, I got distracted with some other projects and am now coming back to this. 

I finally bit the bullet and plugged the computer into the existing C11G board and tried to move the machine, and I got nothing, I had lights on the C11G board (no idea what they mean), and everything was clearly powered, but zero communication between Linux CNC and the actual machine.......The screen indicated something should have been moving but nothing physically moved.

So does this mean I need to create a custom hal/ini file since clearly something doesn't align with the existing pinout file? Or is there perhaps something else going on?

Lights on C11G board:

At this stage, check the bottom row of LED's on the C11 if they light up when you jog the machine, some should just light very dimly, some should be full on when jogging in one direction and full off when jogging on the other direction.

There were no lights whatsoever on the bottom row, so no actual communication/connection to the C11G board?

After another look at the picture, it is there, staring at us, yet i failed to see it, it has a charge pump on pin17!
So edit the existing config using StepConf wizard or make a new one (you can have as many configs as you like/need) and add a charge pump on pin 17, that should kick things ...

Are you using C11G firmware?

If you disable the encoder in pncconf, (setting the number of encoders to 0)
then the associated GPIO pins will become available as inputs

I've got a 5i25 and a C11G. I've read this thread and I've flashed the 5i25 and get a response with sudo mesaflash --device 5i25 --readhmid that makes sense. I added the charge pump logic as suggested without success. I also bypassed it on the C11G board which makes things light up, but none of the motors work then either.
I had this working on a previous computer with a parallel port. I have no LEDs on the 5i25 currently. not sure if that means anything. i tried monitoring the charge pin with hal scope and see it going on and off. Any suggestions?