As long as the box doesn't have rails on top you will be fine. My 2008 has a box about 7" above the rails, only time I had problems was making a 90 degree turn and the rails rubbed the front fiberglass.
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John & Bonnie McClun
2008 F-450 33K "BAT" Big Azz Truck
2011 MS 36TKSB3
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