@Michael_N_Blackwell,
Good to see you back. When I ran your JSON file the devices your M-Z device were there....just have to scroll down to see them as you have lots of stuff! Check the drop down boxes in the Variable Watch and see if they are all there. Have you added any plugins since your last JSON file? I will review it one more time and see if I missed something.
The rooms on the Control tab are not related to the rooms in Vera. I have them setup to handle any dimmers, switches, or scenes that you want in the room. ( maybe I will not use the word "Room" because of the confusion you have pointed out! Lets call them Control Pads)
For Example: You can give the first Control Pad a name Downstairs, after that you can assign devices from the outside, living room, kitchen, and hallway. You can attach any scene you want as well. This format will allow more universal control than just being able to control a single room. If a single room is desired, however, one can set that up as well!
This is just a starting place.....as I get more feedback I will know how to develop it to be a real universal application.
Hope this helps.
Regards
Tim