Front Panel Creation Help

The components that you're creating the knockouts for need to be in the same part as the faceplate because the Intersect tool requires all of the bodies to be in the same part.
You can achieve this using the Join tool to add create part bodies from assembly components.

You might also try using the Indent tool set on 'Cut' as it might allow you to pick in-context references as tool bodies

But here's an important thing to remember: a port for a connector needs to allow access with clearance to both the connector and the socket.
I suggest you check the spec sheets for whatever connectors you want to facilitate and see what they recommend for mounting ports.

Excellent information from John. There are probably a multitude of ways to do this. My first thought was to create a part and use the indent tool with the cut option or combine with the the subtract option. Then I thought of using the mold tool "Cavity" while still in the assembly. Seems to work well. I did try to scale the cutouts but got undesirable results. If you edit your sketch in the virtual part 3 and delete the internal sketches then extrude it to your desired thickness you can make this work. Don't try to scale. You will need the proper clearances and shapes and like John suggested you should consult the spec sheets for the components for panel cutouts. 

Not sure if your case will be sheet metal but I added it just for the heck of it.