Thank you for the great suggestions. I have started working on a few and will post the results as I work through each step.
The spindle cable is a shielded cable although it was homebuilt so it may need to be replaced with a proper cable such as the one Greg suggested. The ground/shield was connected to the Stepper PSU ground although I've now shortened the shield/ground wire and attached it to the VFD heatsink ground. This by itself didn't fix the issue(s).
The spindle cable is currently run through a cable track alongside all of the other stepper and sensor wires. It sounds like this is a big no-no. I'm curious how people avoid this. Every DIY machine I've seen on forums and youtube appears to run the spindle cable inside of cable tracks just as we have done. Any suggestions on how to get the spindle cable routed out of the way and not running parallel to all of the other wires?
Another question I have is with the common ground point. Vlad suggested grounding to a point on the chassis, which I assume means a point on the aluminum frame of the machine. So if I understand correctly the following should be done:
SnapAmp Grounds -> Chassis Ground
73V PSU (reduced from 96V) Ground -> Chassis Ground
Stepper Cable Shields -> Chassis Ground
Encoder and Limit Cable Shields -> Chassis Ground
Chassis Ground -> Earth Ground (VFD Heatsink Ground) ?
KFLOP 5V Ground -> Chassis Ground ?
I should note that our machine frame is made with 80/20 anodized aluminum extrusion, and so it doesn't necessarily have electrical conductivity with every metal component on the machine. If I use a point on the frame for a common ground location it might not be much different than a point on a nonconductive wood box for instance. Maybe someone could explain why a chassis ground is important so I can understand what needs to be done better. Like perhaps attaching short lengths of wire between each piece of the frame so that the entire frame is electrically connected.
Tom, is there a particular 5V PSU that you suggest? Would shortening the output wire on our switching 5V 3A wall wart PSU, and using an extension cord on the AC side accomplish what you had in mind?
I can't say for certain if the problem is caused by a USB communication fault or if the KFLOP is re-booting. However today when I was testing a couple of the suggestions our FLOP crashed again. I have attached two photos of the error pop-ups I received. During a prior attempt to improve things I added a resistor on the KFLOP although it didn't appear to have any effect. You should be able to see the resistor in electronics box photo.
Thanks again for all of the suggestions.
Andy