[drxlcarfreak]

You should not take to much from what you read, they are all in the same boat as you are, they try different things instead of doing the build how it should be done from the start, what I can see by your photo's is wiring plugs Etc which are all problems for a system like this, a layout like this will always have a noise problems

What is a preferred layout? Are plugs not good to have? Are there other quick disconnect options?

[mactec54]

What is a preferred layout? Are plugs not good to have? Are there other quick disconnect options?

Plugs are always a source of problems, direct wiring as it is done in CNC machines Etc is less work and less problems

Start with the filter and new cable, a shield would be very beneficial in your case as every thing is very compact

Some Ideas on how to Ground the Shields

Some VFD Drives already have built in Shield Ground clamps snips below

EMI Glands perform the best for through Cabinet mounting and Spindle mounting for Shield Grounding

So lots of snips for you to look at