>>The USB on the left is for flashing the ARM only, usually you would use soft-update.
OK so if this is covered it won't matter much...
>>The LEDs are visible through the back panel.
I'd prefer to have them at the front of a case so your idea of "using the io patch panel to drive copies of dsk and pwr LEDs" is the better option in my opinion.
>The power switch on the back would be left in the "on" position if it's in case, and either the 5V supply switched, or the ATX power control PCB can be used to switch on/off an internal power supply using the case power button.
That would make life easier
