Located another culprit
 

So, I finally tracked down a rattle that's been bugging me for a long time now. It's an erratic clicking noise that I hear behind my left ear while driving with the top down. I'll spare you the endless tale about my efforts over the past year to isolate the sound, and just say that I finally located it yesterday. It turned out to be a small plastic door (about 2" square) that rests under the leading edge of the tonneau cover. (There's one of these doors on the right and one on the left.) The door moves to a vertical ("open") position when the top is up, and it comes to rest in a closed position (horizontal) when the top is open. It turns out this door is a little loose and can rattle around a bit. I fixed it with a couple of rubber bumpers underneath the door. (See attached photos.) It was an easy fix and eliminated the noise!
Check this if you're hearing a rattle.
Cheers,
Steve