The red rectangle of the PCB design as in post #15 is obviously drawn on the component layer, which means the PCB must be double sided.
If you do use a double sided PCB just call the red rectangle "ground" as you should have done on the solder side. Both grounds are connected physically already via the ground pins of the connectors.
If a 100nF cap on the output creates a short the 100nF cap on the input would also create one.
That's nonsense since a cap won't let pass DC - it will only be charged.
Just build the circuit as planned and rearrange the parts for a complete ground pour for the entire board.
Boncuk