The Ford Explorer roof rack removal procedure is very easy. First pop off the end caps of each roof rail. Pull-on the back of the caps and kind of wiggle them and they will pop off. The center ones are the hardest to get off. The cover wraps around the back edges, but it will come off if You pull hard enough. Take the screws out, slide the rails forward, and remove. I would use clear silicone around the screws and put them back in the holes. The only tools You will need is a TorxBit, flat head screwdriver, and ratchet.
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