Certainly worth trying the easier things first.

I think yours is similar to mine (a Qidi - looks externally very similar, I've had it apart in the past but can't remember the board) - certainly appreciate it's awkward to get to - but set it on a couple of blocks with the bottom off, you can poke a digit or two.

The SMPS - I was actually looking at the SM regulator on the corner of the card - that'll drop the 24V to 5V for the logic, that's the one I'd scope.

Ironically, my previous 3D printers (a RepRap) - it was the USB that was the weak point with ground loops/noise and the card reader more robust (until I tripped over the cable and yanked the micro USB connector off the main board and replaced with a BlueTooth UART, which solved all the problems).