After a bit more looking, it seems I’m dealing with the fact that Jeep redesigned the LJ Sunrider feature halfway through 2005. While my old windows are Rugged Ridge, the frame itself is almost certainly Factory, are are the surrounds. The door surrounds are the later design; the frame that came with the khaki top is the older design.
For now I’m going to leave the brackets/pins disconnected. It seems they’re only needed for the sunrider configuration, which I tried a few times and didn’t particularly like.