So, if Zuvembie knocks Hired Goon to a countdown click, he wouldn't get to place another Zuvembie on the map because he's not KO'd. He's just removed from the map. Unless the Boss is KO'd, then the Goon is KO'd and a Zuvembie can be placed.

Am I thinking this right?

You are correct.

Hired Goon crosses the red line 3 times:

The Boss in not KO, then my opponent wins 40 x 3 = 120 victory points?

or

my opponent only has the victory points if "The Boss" is KO?

40 for each time he crossed the line, so 120.