If i remember right there should be a bolt that goes through there into the rear of the windshield frame so the Hardtop is secured from the front and rear for added stability. though i could be mistaken.
I beleive that to be the primary bracket for conecting the windshield frame to the roof support over the door, . Just looked on mine and the screws were all missing, but the bolted side was still intact as it is easeier that way for top re-installation.( I do know where the screws are too.) The top will probably be removed before the screws are re-installed though.
I think the "pads" in question are weather strip. They go in the corner where the windshield and top meet on the edge where the door shuts. The door weather strip just doesn’t seem to be enough to seal that area and keep it from whistling.