Look you guys.....All he wanted was advise on how to fix the damage. Weather or not you would fix it, is not the point. Either help, or move on.
Like many have said -- a wood (composite stuff won't rot) have it routed out to fit exactly. You may want to look into attaching some 1/4 inch strips underneath. This would be for tow reasons. So you can spray out any grime underneath and to possibly attach some real d rings that will carry a larger load. I would remove the bolts that attach the bed to the frame and use those points ugh larger bolts to secure it to the bed. All that is just an idea -- not sure if it will really work well but vie thoughtof it so I can confidently load my 650lb bike with gear in the back. Those d rng wouldn't last the trip out of the drive of my house. As far as repair -- IMO you would be hard pressed to get it
back to looking like it never happend. Just repaint and you wont notice it as much.