First step is an oscilloscope so you can actually look at what's happening on data lines.
So to me, it looks like the glitching happens exclusively inside the CPU. It appears that I’m randomly experiencing the exact same issue that the PicoEMP in the original article can induce.
1. Stepper and CPU use separate power supplies and are optically decoupled.
2. I’ve monitored min max voltage on the CPU caps and they are fine the entire time, even during glitches.
https://www.rohde-schwarz.com/us/products/test-and-measureme...