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do you have a quad cab? on the older dakotas they had a "stabilizing bar" forward of the hitch. it fits into rubber gromets and when these wear out there can be a rattling noise.
Motodeficient, I had a similar rattle and changed the rear stabilizer links and the noise decreased but didn't go away. So I was able to narrow it down to the shocks. When I had the truck up on jacks I was able to recreate the noise by pushing up on the bed from below. I removed the shocks and the noise was eliminated. So i need to get new shocks. In the meantime I tightened the bolts real tight and the noise is still gone. Hope this helps.
I haven't really looked into it. I have new ranchos on there so I don't think thats the problem. I will get back with you guys once I get some time to investigate. Thanks!