Air flow over bed, is better to cover bed, run open bed or open bed with tailgate off? Truck will be running low 11's down to high 10's. Truck is also lowered.

I would assume a hard flat cover would be best. But make it light so the gain you get from aerodynamics is not lost to weight. Next best would be tailgate off because you are removing weight from truck.

I've made numerous back to back passes with tailgate on, tailgate off...no diff. Trucks can use the extra weight anyway, at least my Dakota can, I have a 58 lb lead brick bolted in the back as it is.
I'm curious about a flush bed covering helping with ET.

Make up some flat iron straps to position the tailgate at about a 45 degree angle. Looks faster, and is adjustable. As said, the weight at the rear of the truck probably won't hurt.

My Dakota was faster with tail gate off. Less weight is what I assumed. But I also had a soft tonneau cover on it and left it on with gate off.