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One thing I just remembered I had to do was make a bushing out of pvc pipe for the left side because my 13 had the power assist gate and the hinge mounted to the box was smaller than the 2000.
I had the same issue with the left hinge on my '08. I emailed Stromberg-Carlson and they sent me a small rubber insert to put in the tailgate for free. If that's the manufacturer of the tailgate, give them a try.