Sounds exactly like the B-pillar issue with the clunk...(electric tape fix) Cant seem to fix it on th tailgate door.. Anyone?

 

I'm not exactly sure if this could be your problem or not, but I had a clunk when o would go over bumps n humps in my tailgate area and it sounded like metal on metal. Turned out the stock jack was improperly stored. Maybe give that a peek?!? It's mention to fit in it's port and be raised just slightly to tightly hold it in place. Hopefully this helps. If not sorry.

 

Thanks for the idea... Ripped that jack out already...

 

Bump.... For more ideas