@Yepher This is perfect! Thank you so much! 
It works perfectly:
(My actual mod called for two circular cutouts for pipe adapter threads, not the big rectangular block that I was using for testing Boolean ops which @KPeter was graciously trying on my behalf to fiddle with.)
How did you do this? Are you running custom code that you might be willing to share?
Also, may I upload your Shapr3D onto Thingiverse to share with others (properly attributed to you here, of course)? No worries if not!