Use SCAD and design a connector for square rods.
 
  The rods are 18.2 mm square. I want to connect two end-to-end.

  make if the bolt holes are created optional for each side - I want to set them separately. Make them M3.5 countersunk

  it's the +X or -X sides I want to turn the screw holes on or off.

  on each of the 4 sides of the connector add additional connectors at 90 degrees. Make each optional