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So after further testing I can tell you that the axis GUI is rock solid. No issues when left for extended periods of time.  When I get some more time I will use SSH to poke around when running GMOCCAPY.

Oh, and on that screenshot, I did NOT run

swapoff --all
systemctl --user stop pulseaudio.socket
systemctl --user stop pulseaudio.service
sudo sysctl kernel.sched_rt_runtime_us=-1

I guess they were unnecessary. (Although maybe I had added that last one to startup in some way before, but I don't remember.)

For anyone wondering when I tried with the R5 340X graphics card, the max base jitter went up to +/-30us.  So I guess that isn't a good graphics card for linuxcnc, or maybe it just doesn't work with the A880GZ and linuxcnc.

Also, in case anyone is interested in, here is a screen shot including the watch of /proc/interrupts when using the integrated HD4250 graphics card with the biostar A880gz .

 

So far, that works!  I don't think I ever would have gotten there without your help.  Thank you.

I didn't end up deleting everything in my grub setup, but I put in everything you added.  The 1090T only has 6 cores, so I reduced the 7s to 5s.  I ended up with:

 smt=1 ro quiet skew_tick=1 nosmt=force mds=nosmt mitigations=auto,nosmt irqaffinity=0-1 kthread_cpus=0 rcu_nocb_poll rcu_nocbs=2-5 nohz=on nohz_full=2-5 isolcpus=2-5 intel_pstate=disable amd_pstate=disable idle=mwait clocksource=tsc tsc=reliable cpufreq.off=1 cpuidle.off=1 intel_idle.max_cstate=0 amd_idle.max_cstate=0 processor.max_cstate=0 nowatchdog nosoftlockup acpi_irq_nobalance noirqbalance default_hugepagesz=1G hugepages=4 transparent_hugepage=never threadirqs forcedeth.use_msi=0 mce=ignore_ce nmi_watchdog=0 audit=0 initrd=/install/gtk/initrd.gz

Not only does it work, it is also running much cooler.  Now the CPU is around 31C, and before it was near 50C.

This result is using the A880GZ with integrated HD4250 graphics.  (I didn't need the R5 340X, but I may try it out just to give others info.)
 

Thank you so much!
 

The PktUART interface is the second serial interface on TB4 pins 19..24
I don't think it needs resistors on the latest board revision, but I would
need to check that tomorrow.

If you want to use the HY_vfd component, you need to use s USB or serial
port to RS-485 adapter.

The process with the PREEMPT_RT kernel is rtapi. The one with -98 priority is the base thread and the one with -99 is the servo thread.
Some settings you could try:
Maximum Payload = Auto > to max
AMD 880 HD Audo = Enabled > Disabled
PME Wake Up From S5 = Enabled > Disabled
PS2 Keyboard PowerOn = Any Key > Disabled
Stroke Key = Wake Key > Disabled
PS2 Mouse PowerOn = Enabled > Disabled
USB Device Wake Up From S3/S4 = Enabled > Disabled
Unpopulated Links = Keep Link ON > Off

And the following kernel parameters instead:
skew_tick=1 nosmt=force kthread_cpus=0-1 irqaffinity=0-1 rcu_nocbs=2-7 nohz_full=2-7 isolcpus=2-7
intel_pstate=disable cpufreq.off=1 cpuidle.off=1 processor.max_cstate=0 idle=mwait clocksource=tsc
tsc=reliable nosoftlockup nowatchdog default_hugepagesz=1G hugepages=4 transparent_hugepage=never
threadirqs forcedeth.use_msi=0 mce=ignore_ce nmi_watchdog=0 audit=0 mitigations=off

Not a problem, hope it was helpful.

Regarding spindle orient... I'd hoped to use orient for my lathe as a 'poor-man's c-axis' once I realized that caxis.comp wasn't doing what I wanted.

I quickly realized that is orient by itself won't hold a position.  You either need a spindle brake, or you need a servo drive that is in position mode (internally).  Servo drives in velocity-mode don't necessarily hold a position rigidly, but LCNC is perfectly capable of treating a position-mode servo drive as a spindle.

LCNC can orient a plain old VFD to a pretty exact position, but that does no good if you're trying to use live tools once the spindle is in the appropriate position.

I think you're on the right track for your first steps.  Get the spindle working as well as you can, then add the orient function.  Orient is simple in concept, but tuning and nailing the position can be tricky and time-consuming.  Especially if you have a heavy spindle/chuck.

Something else to consider... your spindle encoder need not be super-high resolution for spindle/orient functions, but for eventual c-axis work the higher the resolution the better.  And that can become a rabbit-hole when trying to balance high encoder speeds with high resolution... while remaining budget friendly.