I can get that part figured out but I’m wanting to do it with just cut vinyl.
Oh... well, hmm...The trick is going to be the second cut, isn't it. I mean, you'll load up the machine with vinyl and then run it through the plotter. Then you'll take it to the table and weed it, then tape it... and then you'll need a way to get it back in the plotter so that it cuts right.
Okay, here is how I would do it. First, I'd set up the file so that I was cutting the vinyl in manageable chunks, not all at once (so when something goes wrong, it isn't a gigantic waste of time and material). I would add some objects into the 4 corners and send these objects to cut with everything else - this will give you a predictable finished size, because the green stuff will justify differently than the perf outline unless you have something consistent defining the space for both cuts.
Now you'll need to put a long strip of vinyl (I'm using app tape to illustrate) on your plotter where the media feeds out. Make sure it is not going to snag or curl or peel off. Load the vinyl, and when it was ready to go I would set the origin point and mark the edges of the vinyl on the tape.
Cut the green, weed and tape it. The important part here is that you have to remember not to cut the backing paper. You'll need the edges to be identical when you re-load the media.
Load the material back in and line up the edges with the marks you made on the tape. Set your origin point. Send the perf cut file through.
That should accomplish what you need, yes?