I never really found a systematic way.
I gave up when I found all the measurement programs to show not only different but contradictionary measurements.
Also, my mesurements using external hardware I hacked together - like comparing a software-generated pin-toggle in every cycle of the base thread to a frequency generator - did not help.
I was also unable to rebuild even an official kernel - that is: one shipped with LinuxCNC.
I can confirm, that all Nvidia graphics I tried are making the PC useless for LinuxCNC.
Stay away from anything Nvidia.
The Radeons work well for me.
One reason I was able to identify through elimination: when I swapped an older hard drive for one supporting SMART, a perfectly fine working controller became useless.
Turning off SMART support in the BIOS Setup fixed it.
Obviously, handling SMART diagnosis has a higher priority than the timer interrupt - which it should not have.
As a result of all my frustration I just switched to Mesa FPGA cards for step generation.
Their documentation was a bit confusing at first, but eventually I figured it out.
I have one controller with a PCI FPGA card and the Mesa driver/breakout card, another one with just the (cheap!) FPGA card any my own little driver/breakout board.
In both controllers the base thread is now empty except for a pin toggle on a parallel port. I feed this 50%-duty PWM to an external watchdog (a window comparator checking the analog voltage to be between 40% and 60% logic level of the parport tripping an RS-Flipflop; so if the base thread stops completely, the watchdog turns off the power to the drives and spindle).
A bit of jitter in this function is no problem (covered by the rather large window) and the FPGA make silky-smooth steps
Any btw: I stocked up on Core-II-Duo based Dell Optiplexes and Fujitsus when they were still available.
They have enough CPU horsepower for LinuxCNC with Axis and perform much better latency-wise than anything more modern I tried.
The more nifty stuff the chipset has built-in, the more hickups the BIOS seems to be able to cause.
But again: sorry, I have no systematic, just anecdotal evidence.