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Instead of removing the existing roof rack, use it to incorporate the boat tail by building the roof line up to make it the new highest point as far forward as possible using the template. Then only a small portion behind the rear of the vehicle will then stick out. Think of it as a hump back whale.
You could use the existing side rails to flex a piece of coroplast or 1/2" insulation board in between the side rails to the shape required, attaching it with zip ties. Then use EMT or aluminum pipe to build a frame behind the vehicle to finish the tail.
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