I don't like throwing new parts at a problem but I have no idea on additional tests, diagnostics are re-wiring I can do to resolve this issue.
I am now down to a minimally configured G540. Shielded wires (with proper shield grounding to the steppers) and no other connections other than power in the control box - which is an aluminum box and the enable pin to an e-stop (and I did test jumpering this to eliminate noise from the switch and wiring). The power supply is a quality 48V Mean Well (I use these on all my CNC machines). That's it, no other wiring in the box. The PMDX-411 is connected to the G540 outside the box and the USB cable runs to the laptop. I suppose I could go full-monty and wrap the USB cable with copper foil and ground it - DIY shielding - but I am not convinced that will help.
So, with this configuration, I can jog. I can't home of course since no home switches are connected. I do not have the probe physically connected but I do have it configured in M4 and the 411. So, in theory, a G31 command should at least make the Z move. But it does not, M4 screen shows the odd dimming and then just sort of hangs. It is still responsive but I have to click the reset button to get control back. And then about 1/2 the time, this causes the 411 to disconnect.
I agree with Bill about USB, suboptimal for sure. But I'd really like to leverage the G540 and the control box I've already built (and had working for several years). The ESS is compelling but I don't need support for multiple parallel ports. I searched and didn't find a simpler, 1 parallel port equivalent. Maybe someone here has come across one? That would be ideal to convert an existing simple G540 based system to ethernet interface.