Scott, the stone sits flush in the panel. And yes decreasing the gap between the 2 stones helps with upper heat and crust browning. That was the first suggestion I made to JRo. I've got it down to 2 3/4" now but in only making 11" pies. I may need to make 14" pies.
Chau, that's exactly what I'm counseling against. I'm talking about lifting the stone off the panel by 1/8", max. As you go higher, you lose the deflecting qualities of the panel, as Jro saw when he lifted his stone as high as you have it.
I'm not entirely against lifting the entire panel to close the vertical gap, but, as of now, I think raising the stone that high off the panel is a bad idea. 1/8" max- stainless steel washers.
Also, due to the fragility of the stones and the cracking that has occurred, I think it's possible that the stone this ships with might be a fibrament-ish cast refractory rather than the more durable kiln fired cordierite. If that's the case, then I'd stick with the stone they give you because the conductivity will be lower, which will slow down the bottom bake.
Now, everything we're doing might end up handicapping the bottom too much, and the strength of the burner might not be able to pump out enough BTUs to compensate, but it's worth trying- for those that don't mind the remote possibility of melting their oven
Speaking of which, I'm not entirely certain what role the aluminum cover plays in this setup. Perhaps if the top stone doesn't sit flush in the shield, the cover traps escaping hot air. If there aren't gaps, though, and one were pushing the oven to higher and higher temps, I might lose the cover, and, if there are gaps, you might want to track down a steel plate for a cover- perhaps 1/16" thick.