I think you're taking a huge risk by using the factory roof rack. I'm sure they weren't really meant for holding that much weight. Yeah, you've made a couple of successful trips without incident, but in my opinion you're playing with fire.
The used 2007 CX-9 we bought has some scuffs in the black portion of the rear bumper.. not sure what from, could be anything. I'd like to touch it up myself, but I'm unsure what to use that matches the rest of the black trim. I'll probably sand it down first to smooth out the scuffs, and then...
It's a little more in depth than just going out and buying some stuff off the shelves, but I just wash with regular cash wash first (I use Meguiar's Gold Class car wash), then get some Meguiar's Hyper Dressing diluted to a 2:1 ration and spray it on a microfiber cloth and rub it on the black...