Look at the design now compared to the original.
Soo much improvement 
the only thing that bugs me right now is the ergonomics/// all those connectors, are you going to want to remove them often and individually? they clips will be blocked by the other connectors
Those look like friction fit JST connectors, shouldn’t be an issue.
I’ve only had the prototype board out of the box once in a year, so, no. Once in place it should stay in place.
Do these shielded chokes are part of DCDC or are just a filters?
If it is DCDC then I would remove GND copper on top just under them to reduce the capacitance that has to be reloaded in each DCDC cycle. That will reduce a current peak pulses in each cycle that can be source of unwonted EMC emission.
Zone at other layer is (in my opinion) enough as shielding electric field. I am simply more afraid of the emission of a magnetic field in this situation than of an electric field but I’m not sure of my opinion.
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