I recently got a 10' Pelican Brume sit-inside kayak. So far I've been transporting it by simply rolling down the back window and stuffing it inside.
The nose is nestled against the back of the passenger seat and the center console. I put an old hand towel there, and another under the boat where it contacts the bottom of the hatch window opening.
My 4Runner was already set up for sleeping inside. So the bottom part of the passenger-side rear seat is removed, and that seat back is always folded down. I have a platform made of two boards there. For kayak transport I just take out the sleeping bag and foam pad.
So far I've only strapped it down toward the front, utilizing the OEM D-ring for one end and the outboard seat belt bolt for the other end. (The seat belt is unbolted and rolled up out of the way since there's no seat there anyway.)
Next time I go, I'll be using a 5 mm cord toward the rear. Each end of the cord will attach to the rear D-rings. I'll be utilizing a Nite-Ize CamJam on one end so I can easily reach in the open rear window and pull up on the cord to tighten it.
This approach works fine for getting to the local water hole (Lake Mead), including some freeway driving. But since the rear window is open, I wouldn't be comfortable making longer trips. Both due to possible weather issues, and security issues.
BTW, I stopped using the flag on the back of the kayak, since in Nevada it's not required unless there's 4' or more of overhang.
I did a lot of flatwater kayaking in the past but got out of it years ago. Due to injuries, etc. in the interim, I'm not sure if I can handle the repetitive stress of paddling. If things work out, I'll upgrade to a bigger and better boat. I'll probably get a trailer because I don't want to struggle with putting a 50+ pound boat on the roof, but I'll want to travel to other water holes. I like the Yakima Rack-and-Roll, since then I can also put my Yakima cargo box on it. Plus it folds for storage.
P.S. Speaking of injuries, Timothy, that x-ray looks brutal!
(Click for bigger pics)
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Candace66, on Flickr
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Candace66, on Flickr