Hey BB, sorry I forgot about this. I meant to comment back when you first posted, but obviously got sidetrac.... Oh look! Another Bronco!!! ;D
Anyway, that looks like a driver's side (left) to me, where the "lip" or flange goes rearward up almost against the tailgate and facing inward toward the center of the tailgate.
The upper part in your picture with the two larger holes is up, with the bend aiming forward.
It attaches to the corner pillar with sheet-metal screws, while the larger holes tie into the hard top.
The rubber gasket will slip over and glue to the flange so that it butts up against the tailgate and seals.
The seal itself is a full-length long seal that encompasses the entire rear of the truck. From one corner of the tailgate at the floor, up along the entire lift-gate and then back down to the far lower corner of the tailgate.
For this reason, it's best to find the center of the seal and mark it. Then start there in the center of the hard top.
Oh, and we actually call them things "ankle slashers" because when the hard top is removed, they stick up just right to catch the ankle or calf of an unsuspecting passenger piling in or out of the truck.
Nasty bit of work that!
So if you intend to run with the top off, go ahead and set them up for install, but mark each one where it crosses the top of the bed and just cut it off and be done with it.
You're cutting the seal in the same place anyway, so that the lower half will stay with the truck, while the upper half stays with the hard top.
You didn't figure that out in the last week? ;D
Busy with other pursuits, eh?
Paul