I decided to go ahead and make a mess of my rear fenders before I sent them to the body shop. Here is some evidence of my attempt at tunneling in some taillights.
1. I got the bed even and found the center of the tunnels.
2. I tried to follow the advice of a bunch of people online and I watched the episode on "Trucks" where they installed a set of tunneled taillights. I measured about a thousand times and still cut the hole a little to low on the drivers side, I ended up having to fill in a small gap. After about a thousand tac welds I tried to get a bead around the tunnel. I know absolutely nothing about welding so be as critical as you like, it won't make it any prettier.

I literally spend three hours on each one trying to get the tunnel to fit in parallel to the bed side before I welded it in place. I ended up having to shave a significant portion of the side of the tunnel.
3. I ground off the beads and taped it off to copy on the other side.

4. Duplicated it on the other side. Then cleaned it up a little with some filler.
5. I just sat the taillights in the tunnels to see how they looked. I'm going to take the fenders to a body shop this week or next and maybe they can fix some of my screw ups. You can see on the close up shot that I couldn't get my grinder in close enough to get the small ridges out. I needed a more precise tool.