@Jules V. I recommend your first setup, here’s why:
The most ideal way to cook a pizza is to balance cooking rate of pizza top and bottom by balancing the heat below and above the pizza stone.
With the high intense heat being located below the stone, the goal is to limit that bottom heat to the stone so it will be hot enough to cook pizza bottom at the same rate as the heat above the stone will cook pizza top.
And since the heat above the stone increases as we get closer to the lid, it is best to position the stone as close as possible to the lid top to take advantage of the highest possible heat available above the stone. But, at the same time we don’t want to be too far from the charcoal flames where the stone is not getting enough bottom heat.
MPS comes with feet that will raise MPS by ½” and extension legs for additional 3” to bring pizza top closer to lid top heat.
I would use MPS with the ½” tall feet and place it on your secondary rack set at 3 ½” high, that will position the stone about 2 ½” form the lid and about 4” from the charcoal concentrator flames.
I am not sure if cracking the lid open is more helpful than harmful. I think cracking the lid will allow for lots of heat to escape from the bottom where we want all the heat to flow over the pizza on its way out through the lid vent’s. Any way try both and see what works best for you.
Also, you may want to cover open area around your heat concentrator with aluminum foil to maximize amount of air flowing through it.