I am missing some fundamental basic thing with Inkscape. I believe my need is simple. I want to make cut paths for an overall rectangular object that has one square and a bunch of circle cutouts inside it. I have created the shapes as I want them in layers and just need to apply the cut paths. I am guessing I need someone to hold my hand for maybe 10 minutes on a discord video call with this and I would be all set. The desired end result of the physical thing is below. Please message me if you are willing to help. I will share the rend results if others want this for themselves.
The working file is: