Thanks for posting. And you're right, there is very little documentation out there. We're all writing the book as we go.
Two things I would note...
You state, "The stop button currently has a bug and will animate even when the process is complete." It is not a bug. Apple Configurator is designed to work continuously so that you can unplug and replug new iPads anytime and the Prepare process will automatically start on the new iPad. Its very helpful when you are "imaging" a bunch of iPads not to have to click a start button each time you want to start Preparing a group of iPads.
Also, I would recommend making a backup of the first Supervised iPad as sort of a "golden master." That "golden master" could include WiFi passwords, MDM enrollment webclip, Safari bookmarks, wallpaper selection, and screen arrangements among other things. Then restore that "golden master" backup to all the other iPads. If you have iPads 2, 3, 4, etc all plugged into the cart (or other syncing device) you can apply that "golden master" backup to all of them at once, and then add additional apps and configuration profiles. It'll save you some time from doing it one by one.
Hope this helps and good luck with your deployment!