Alpinegroove, while it's very encouraging that you can achieve beautiful top color in 4 minutes in a bottom heat source scenario with a top stone on the upper shelf, cast iron is too conductive as a hearth. In bottom heat scenarios it's critical to slow down the heat transfer on the floor rather than accelerate it with a relatively highly conductive material.
Based upon the burning you're getting on your undercrust, you might be able to get away with a thinnish cordierite (kiln shelf) hearth, although quarry tile would be considerably cheaper. The one thing I wouldn't do, though, is swap the top and bottom stones. The top stone is working perfectly, I wouldn't mess with it. I also wouldn't change the size of the bottom stone- I'm guessing the ceiling stone is larger, correct? The larger ceiling is another important facet as it helps to collect the heat rising up from below.
The oven is definitely running hotter than the dial temp. If you could score an infrared thermometer, it would go a long way in determining what you're working with.