I still have K-mart roof racks I used on my 1969 Dart. I had to fab aluminum channels to support the edges so they didn't cut into the vinyl top and filler above the drip rail. They came w/ just rubber coating on the steel ends, which was dumb. They also whistled loud, starting at 50 mph. For my canoe, I later found it better to use foam pads that slide over the gunwales. That kept the canoe from sliding around and better carried the load. But, kayaks don't have gunwales. The foam noodles sounds similar. Perhaps cut slots in them so they don't slide on the kayak. I assume you will load it upside down.
