Spindle Step/Dir servo ramp down before stop on M stop command.

Neat test setup!
I got the component compiled ok.
Things don't work yet , current findings below, but I want to go through my ini/HAL files compared to yours very carefully - presently all jogging does not work ( jogwheels, buttons, etc) - your HAL file is one or two revs behind mine so there may be deltas.

So far, with some items just observations, and others more relevant:
AXIS display now only shows 3 dots representing each axis, and also only 3 DRO's numbered 1-3.

Then, Homing fails.
HOME ALL
X homes OK, to home sensor, etc.
Y starts going away from home sensor, and VERY fast - so much so that the servo stalls with a bang..
C axis - if C was say 100deg away from index, it slowly rotates to index, goes past, and oscillates again, till stopping @ index.
- if C was close to index, say 20 deg, it goes to index slowly, and stops. And the movement is VERY slow towards index.
After this, Jogging on the AXIS screen (via Mouse) works for X, Y has failed stalled, and when I try jog C it starts turning very slowly, and just carries on turning.

I will attached the latest ini/HAL files as soon as I have gone through them carefully again.

EDIT:
I have been through the files - I see no obvious differences in the non-C axis related sections - X and Z are as was, so not sure why the homing of axes causes Z to start wrong direction and accel till stall.

Lots of delta in the C_axis sections,, with stepgens added as well...
in KINS, KINEMATICS has kinstype=I added - correct?

Edited HAl and ini are attached - have changed 5i25 card to 7i92 as well

Which INI file are you using? You should probably mainly be using your existing one.
Also, make sure than nothing regarding joint.1 crept in to my new HAL bits.

The encoder scale might be wrong, if you are using the value from my INI.

Am using 'my' ini - merged your changes. Axes x,z and spindle as in my ini, basically unchanged.
Ditto the HAL file, so at present no idea why Z axis homing is messed - The Z axis does not start going to the home sensor, it starts in the opposite direction ,runs very fast and stalls within a few mm of movement.

My encoder is 4096 - seems that is the same as in your ini...

I have compared line for line ini and hal so far - will test on the lathe again in the morning, also why the jog wheels don't work after trying to home...
I did try again with the previous hal and ini ( before the version we gave up on) and that still runs ok - home all is ok and jog wheels work, etc, so hardware is still ok..

The Z axis does not start going to the home sensor, it starts in the opposite direction ,runs very fast and stalls within a few mm of movement.

Very strange. Possibly you changed the home pin sensor assignment and the new HAL has reverted?

No changes made - I used the HAL/ini files just before we gave up on that config to check , and all still works. I did check all the pin assignments under 'external inputs' in HAL, all unchanged and correct so far. Still digging..

Otherwise, check the [JOINT_2] *HOME* velocities.

Why [JOINT_2]? That is 'C', not Z?
[JOINT_1] ( and 0) are unchanged from previous setup.

why the jog wheels don't work after trying to home....
That is because the machine is stuck in "joint mode" and I don't think that the HAL is set up for joint-mode jogging.

Where do I verify that? If it is so, I will dig in the docs to see if I can set it up..

This confuses me somewhat - in the [JOINT_2] Section of C_axis, HOME_SEARCH_VEL = 0
The Docs say:

If a joint does not have home switches or does not have a logical home position like a rotary joint and you want that joint to home at the current position when the "Home All" button is pressed in the Axis gui, then the following ini entries for that joint are needed:
HOME_SEARCH_VEL = 0
etc

Are we trying to Home at the 'current' position? I thought index was the home pos?