If you have a LimitedHDx edition on your Ford, and you are having issues with end caps getting smashed by the tailgate, here is how you can get that situation resolved.
From inside your truck bed, with the tailgate shut, you will want to loosen the bolts on your Box Link system at the tailgate end.
Once loosened, nudge the rails up just a bit. Check the positioning of the end cap and see how it sits on the tailgate. It should be sitting evenly on top of the tailgate.
Once you have the end caps sitting flush with the tailgate, retighten the bolts on your box link system.