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In all honesty it may be worthwhile going back to you original setup. I generally think of the PC for a cnc setup as a "black box". As along as it doing everything you want leave it that way.
But it is quite curious as to why backlash is not working as expected. Maybe raising an issue on github may get better responses. The guys that do the coding will be answering.

I hate to say this but backlash comp should be a last resort after you have exhausted all mechanical ways to reduce it.

Sorry I haven't been able to solve this issue and I wish you all the best. If you do find a solution it would be great to describe the fix for anyone else in the future. Good luck as always.

Your ini file is a mess and very hard to follow, but:
Y axis/joint has unreasonably big ferror and min_ferror values, probably should be close to what X axis has
Backlash_speed is set at 6000 inch !!!
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What is the drive train? Belt? Screw? Ball screw?
Since it is a laser, i would advise belt only on X and Y.

Try jogging with on screen buttons, does it still jerk?
The wire you connected 24V is the machine enable, so it goes to Mesa 7i77 output, while the other wire should go to input as machine is ready. Does the other pin come from the ON/START/GREEN button?
Tuning does not seem OK, but it is very nice that you can jog at low speed, try increasing the speed gradually and see this for further instructions:
forum.linuxcnc.org/10-advanced-configura...ning-detailed-how-to

I Tried with 'hal_pi_gpio.write base-thread' at the end of the base-thread, but it does not make any difference.
Thanks for the info anyways.

No double posting.
And fix the tittle to explain what it is about.
Thank you.

I can't find much on Ethercat homing. Maybe I'll be able to figure it out down the road. How would I set it up with Inputs on the EL1008 instead, in the meantime?