3/8", wow... that is pretty tight. Here's what I suggest trying, Jay. Put the stone in the bottom oven, second shelf from the top. Pre-heat it to 500 with the convection feature on for 45 minutes- with convection, that should be plenty enough time to pre-heat the stone. After that 45 minutes is up, take temps of the ceiling, the top of the stone, the bottom of the stone and the oven wall beneath the stone. If all the temps are pretty close, your air flow should be alright. If they aren't (ie, the ceiling is noticeably cooler)- do you know anyone with a grinder or a circular saw with a masonry blade?
Don't worry about the clearance on the back and front. You don't want to lose any of that precious real estate. As long as the door isn't touching, you're fine.
Don't sweat the distance from the ceiling too much. The top of my stone is 5" from my broiler, and, once in a while, when I tilt the peel to launch the pie, it feels a little cramped, but most of time it's okay. If your opening is between 5" and 7", you should be fine. I was hoping that moving my pie close enough to my ceiling would mean that I wouldn't have to use the broiler, but I have found that my ceiling doesn't give off much heat- at least not in the 4 minutes that I'm baking my pizza. Until I put in a ceiling stone, I really have no choice but to use my broiler. With convection, though- that's a different ball game. Convection gives you considerable top browning without broiling. Assuming that 3/8" clearance is giving you proper air flow, I would definitely bake your pizza using the convection feature. For today's dough, I would try 500, with convection, for 5 minutes, with a check after 3.5.
The dense crumb you were getting is typical for KABF. Like I said before, you've got the best stone money can buy, now it's time to graduate to big league flour. http://www.restaurantdepot.com/misc/locations.aspx#midwest
There's a Restaurant Depot in Columbus and Cincinnati:
270 North Wilson Road
Columbus, OH 43204
4501 W Mitchell Avenue
Cincinnati, OH 45232-1911
If neither of those is close, I'm sure that a little research will produce a local bakery supplier.
You're doing an overnight ferment, correct? I think your yeast quantity might be a bit high. Are you getting much volume after a day? Doubling? Tripling? Unless your working with feeble yeast, I would trim that down a bit. The flour is really the most important aspect, though- once you get your hands on real pizza flour, then we'll cross the yeast bridge.