factory roof rack part of the solution
I carry two 17' canoes and the limitation of the factory rack is the narrow distance between the front and rear crossmembers. I need wider spacing.
On my Tundra, I use a 72" Yakima crossbar secured to the camper shell for the rear bar, using 2 control towers and Landing pad 6/7 secured to the camper shell permanently.
On the front, I use another 72" Yakima crossbar secured over the cab with Yakima Q towers and Q Clips specific to the vehicle.
On the 4Runner which I just bought yesterday, I will use Yakima Lowrider towers to attach the 72" crossbar to the factory side rails for the rear crossmember.
Over the front doors, I will use the Q towers and Q clips and a 72" bar. I bought the Q clips a few years ago anticipating I would get a 4runner. I'm not sure what number they are, they are not specific to the 4Runner but the word was the Q clips for Tacomas would work so I bought those.
Not great pics, but the Tundra is shown with even bigger canoes and the front bar over the cab. The Subaru shows the Lowriders hooking to the factory side rails. So on my 4Runner I will use those same parts, mix and match.