Novakon Mill Conversion - Getting Started

Pin 14 is a PWMgen for compatiblity with the C11G breakout
(it would be PWMgen 0 in the hal file)

The stepgens are addressed as stepgen 0,1,2 etc in hal
These go to appropriate C11G pins (look at the pinout file
or the results of a readhmid command)
For example, Stepgen 0 is connected to DB25 pins 2 and 3 (step and dir respectively)

The optional qcount can be ignored, just use the GPIO inputs

IO Connections for P3
Pin#  I/O   Pri. func    Sec. func       Chan      Pin func        Pin Dir

 1      0   IOPort       None
14      1   IOPort       PWMGen           0        PWM             (Out)
 2      2   IOPort       StepGen          0        Step            (Out)
15      3   IOPort       None
 3      4   IOPort       StepGen          0        Dir             (Out)
16      5   IOPort       None
 4      6   IOPort       StepGen          1        Step            (Out)
17      7   IOPort       StepGen          4        Step            (Out)
 5      8   IOPort       StepGen          1        Dir             (Out)
 6      9   IOPort       StepGen          2        Step            (Out)
 7     10   IOPort       StepGen          2        Dir             (Out)
 8     11   IOPort       StepGen          3        Step            (Out)
 9     12   IOPort       StepGen          3        Dir             (Out)
10     13   IOPort       QCount           0        Quad-A          (In)
11     14   IOPort       QCount           0        Quad-B          (In)
12     15   IOPort       QCount           0        Quad-IDX        (In)
13     16   IOPort       None

I should add that if you are creating a hal/ini file set from scratch with pncconf
you should use pncconfs discover option and set:

encoders=0
stepgens=4
pwmgens=0

and then all the required GPIO will be available to setup in pncconf

I am going to first start this off with a huge thank you for the consistent feedback and answers. And secondly an apology for so many basic and somewhat repetitive questions.

I understand the motor setups and stepgens and can follow those in the hal file (mostly). But I am still a bit confused on things.

My C11G board is currently wired to my Novakon and is fully functional with MACH3. My goal is to plug into the C11G board as is already wired to the mill; so when I read the pin assignments from the C11gx2 pin file and the hal file, I have concerns on the functionality of the Axis homes and E Stop. My X, Y homes and E Stop are are physically wired to the pins that are listed as optional QCount in the pin file and when in PNC config I don't have enough GPIO options to assign these otherwise. What I am trying to understand is how to account for X home, Y home and my E stop when they are wired into the board already to pins I can't assign but are also not the correct function....

Do I need to create a hal/ini file from scratch ?

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:

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

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?

its normal for no light to be illuminated on the 5I25

Can you post your hal/ini files?

Here are the hal and ini files. Thanks for the reply!