has anyone made a custom roof rack for a truck with a cap on it? if so how did you mount it?

I don't have one but I've seen one. The guy had a Yakima rack with rails for adjusability. The rails ran the length of the cap.

I've seen on both the Yakima and Thule sites that you can do that or mount fixed "feet". Personally, if I'm going to be drilling into my cap roof anyway, I would rather have the rails.

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Sgtsandman's Work in Progress
2011 Ranger XLT, 4X4, 4 door Super Cab. 4.0L, 5 Speed M50D-R1HD, 3.73:1, 8.8" open differential, Jason Pace cap
2019 Ford Ranger STX FX4, Super Crew, 2.3L Ecoboost, 10 speed automatic, 3.73:1 with rear locker, Leer 100XR cap

Are you looking to put the rack on the truck cab or the actual cap?

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I'm in the same situation since I started a job that requires me to carry tools, supplies, and ladders. I recently bought an ARE cap, and I have to find a way to add a ladder rack.