I have carried a canoe on the stock roof rack for 1000s of miles and it has worked out fine.
I recommend:
- Use closed cell foam pipe insulation (similar to pool noodles) at the points of contact between the boat and the rack.
- Tie the bow line and the stern line from the boat to the front and rear tow points to prevent fore and aft movement of the boat. You want these to be tight, but not too tight, so they do not stress the boat's hull when you go over bumps. Maybe use a length of rope between the left and right front tow points on the LC, then tie the bowline to that loop. I offset the boat about 1 foot off center to the passenger side for better driver visibility out the windshield.
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Use old bicycle innertubes to secure the boat to the rack. The rubber tubes have some stretch to absorb shock, but they are strong enough to hold the boat in place. You will need several old bicycle inner tubes.
The only mishap I have had was when using ratchet straps to secure the boat to the rack. The straps were too tight, and the ratchet mechanism damaged the hull of the boat while driving on a potholed road at speed. That is why I recommend using the bicycle innertubes instead. They are soft and plaible, yet strong enough to do the job.
The main thing is to tie the boat on tight, but not too tight. You want to allow for a little movement when you hit bumps or wind gusts. The combination of the foam noodles under the boat and the rubber innertubes act like a shock absorber for the boat so it moves alittle bit instead of stressing the hull.
In my experience, the stock roof rack works fine for carrying a canoe. You want to keep the canoe down as close as possible to the roof to minimize air drafts under the boat while you're driving.
Yukon River; Circle, Alaska. July 2012.