I have a 16' canoe and a '14 FX4 with the 5.5' bed with the Extang Trifecta folding cover (that sits on top of the bed rails).
I installed the Back Rack with the c-clamps that allow it to sit above the cover, and I use the hitch-mounted Extend-a-Rack in the low, farther extended position so the canoe sits on an angle above the roof and just barely clears the closed tail gate.
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https://backrack.com/spec.aspx?specList=0
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BACK RACK - 15024 https://www.amazon.com/s?k=Backrack+15024+Frame&i=automotive&ref=nb_sb_noss
TONNEAU ADAPT - 50112 https://www.amazon.com/Backrack-50112-Tonneau-Cover-Adapter/dp/B01GWD2OVG
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It's too dark for pics now... and the Extend a Rack is still buried in the shed... sorry.
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I'm not sure if you can fit all three boats on this setup... but if you look at some of the hitch-mounted ladder racks, you might find something that is wide enough to fit all 3.