Help me find where this is coming from

Can you show what exactly you're doing to the bed to make that noise? Now it's hard to see since it's only a closeup of your hand and the camera shakes when you move. Lay the camera, your phone I'm guessing, somewhere so it shows the bed and then shake the bed or have someone else take the vid for a few seconds while you go from side to side. It might help to get a different perspective of what is actually going on.

 

This, or its your tow hitch receiver.

 

I had trouble with one of my bed bolts. It would tighten down against the bushing but not against the box as much as it should. I think that the bolt was bottoming out. Try watching the washer under the bed bolt when you flex the box, you'll probably see one of them move. Maybe this is the problem that you are having too.

 

Before you cut anything, tighten you spare tire against the bed using the hardware in the rear underseat storage compartment.

it could just be you spare fire hanging a little loose.

 

Tape up the loose parts on it first then recheck if sound is still there. That would suck to get rid of it and still have the noise.