I have a 14' redfish too... and mostly likely the vibration sound is the ropes/straps you're tying the boat down with. Those things can give a good hum. The bungies over the rear cargo area wouldn't make that sound... they'd have to be hitting something.

Also, I transport it bow forward and upright, and have never had the seat flip up. the wind will go right over it due to the shape of the boat. Not really something to worry about (of course, I write this and now will have problems). I use straps to tie the boat to the roof rack, and then one line from the bow to the front of the car. You don't need to crank down this bow line, as it's really just there incase your roof rack fails. Putting a line from the stern is overkill, in my opinion (obviously won't hurt anything either). But do crank down on the straps that attach the boat to the roof rack.

I use the yakima cradles with my redfish (cradles in front, rollers in back), as the boat is a little awkward to put on j-bars. I would have gone with the thule cradles, as I feel the yakima rubber ones sort of flex too much. I have malone j-bars and they work well for my other kayaks. I think malone makes a cradle, right?

Good luck and have fun on the boat... it's a very stable fishing boat. Get used to leaning over the side... you'll really have to try to fall out of it.