7i76e pin configuration, flash firmware, do it in HAL files, etc. ???

I do not have a spindle drive manual available, but I do have some documentation:

Pin out:
 

Wiring Diagram:
 

I Think this is the logic capture from the spindle.  I may not have saved the best file from that but it appeared to be PWM, 
 

Here's zoomed into the logic capture:
 



I do need to stress I did not do a perfect job organizing and storing my logic captures and I may have made a mistake but I am pretty sure that it was PWM, but without having access to the original controls anymore it's impossible for me to tell

if you zoom in on the signal from the CK pin this makes me believe it's PWM:
 

That looks like constant 50% duty cycle but variable frequency
so a standard stepgen should work.

^This makes sense, it is right at 50%.

I'm not confused about this part anymore, but, how on earth do I configure everything else? like the enable, how to I use the two wire signals to know theh servo is ready, etc? Do I work on a custom HAL file? Does the "actual frequency" go to an encoder, or do I just make some kindof input for it using two pins?

Enable could be driven by a spare step/dir output (if one more is free)
The driver ready can be read via the sserial RX input pair on the 7I76E
(assuming you are not using it for I/O expansion)

I don't think the "actual frequency" signal is of any use to LinuxCNC

Cool that makes sense! I should have thrown in here that there's also all three axes motor drives that have the two wire outputs for the ready signal, so 4 sets total. Not sure there's enough serial ports for that but I'll look.

One weird thing about this machine is it has an index signal, and not an encoder signal, for each axis to make sure it's in sync. If it didn't detect the pulse when it knew it should it would throw an error. Not the best of setups as it only happens once per ball screws revolution. But better than nothing. It's a three wire sensor, I can't remember the name but it senses when this piece of metal (or magnet) moves by.

It also seemed to use these in the homing sequence. It would hit the limit switch then back off until it got that pulse.

Would this require custom programming or could I somehow set this up as an encoder?

I'm glad you came here and I see the experts have been helping out.
With less than simple system to set up you really need to edit your ini and hal files yourself as pncconf is just for a basic config.
Think of it as the ini files defines the fixed part of your machine that does not change and the hal file is where you "wire up" the machine to Linuxcnc which often accesses the data in the ini file.

With regard homing, its covered here
linuxcnc.org/docs/devel/html/config/ini-homing.html
Take your time here to understand it.

You should not need custom programming but if you understand C its easy to write your own components.
See  linuxcnc.org/docs/devel/html/hal/comp.html
You may need to do some work in hal to work for your hardware. Eventually it will all click.

But the first task now is to work with PCW to get your motors moving!