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I've never used rtai, but run latency-history and htop, sort by priority (F6?) and you'll see. I think you could use the same script.
Bad RAM memory could be a cause, usually using 2 ram modules (of the same) is better so it can use DDR. But if one of the two is bad removing one or the other might give a better result.
HDD can also be a cause, if you still use that buy a cheap SSD.
Disconnect any CD/DVD drives, SD-reader units.

1. Your ini is missing the spindle section while your hal references 'SPINDLE_9' ini entries. Looking at your hal file makes me think that you are not actually using a spindle setup. If that is the case then you might want to completely remove this section from your hal:

Yeh, that's the one! I made some enhancements for it and Les added it to Sheetcam. There are some settings at the top of the post to check and turn off. I made it so Sheetcam was the master seeing it was for his system

@ihavenofish
Wow that's nice. Having 3 ton machine moving like that also with the current jerkness is too scary definitely not good for my heart.
@LCR
I have similar issue with non-ethercat drivers. you can check it out this thread. It may help
forum.linuxcnc.org/38-general-linuxcnc-q...s-creeping-up#309973

I converted the bcl-amp output to a differential signal (max485), at a long length it works much more stably and reliably. You should do the same (I understand that your frequency is linear and depends only on the height). A couple more questions, your sensor have temperature stabilization?

So, I dug out my 14-year-old 6040 CNC again. 
I already retrofitted that thing once, tossed almost all the original electronics and went with G540 and some old industrial PC. Still, I was strapped for money, and it was a hack. I only used it occasionally for a couple of years, then it just collected dust. 
A few months back, I found myself in a situation where I had a lot of time, and I'm no longer that strapped for cash either.
I got myself a new set of closed loop steppers and CL57T drivers from SteppersOnline, MESA 7i96S board, proper PSUs, a new mini PC and nice steel enclosure, and I'm trying to push hard to do it properly this time. I have a physical layout somewhat complete but still grinding the schematics.

Would somebody be so nice as to look it over?

I have the following questions:
1) Is it ok to use 5V to enable stepper drivers (OUT0)? Stepper drivers will be configured to use 5V, but I'm assuming that DIP switch is only for STEP/DIR pins.
2) Since I'm feeding 24V to IN COM, I have to use 24V to detect alarms from stepper drivers. Is it ok to mix 24V and 5V on the same driver for different functions (5V for enable, 24V for alarm)?
3) Can I detect driver alarms with just one input? Any practical benefit have them wired individually?
4) Right now, I have all limit switches wired independently, but I really need that? Current setup has them all in series on a single wire. Is there any practical benefit of having the wired separately?
5) Not sure about E-Stop. In the schematics, it kills the VFD power and sends a signal to the controller. But I'm not sure about that at all.
6) I have two input pins left, but I still need a probe at least. Am I missing anything else? 

Thanks a lot for any suggestion.

To the OP just for reference next time could you specify if you are using a RPi4 or RPi5 so if we need to look at the images it makes life easier. As both the 4 & 5 come in B variants.

Cheers
Rob