Ok here is the finished product.
First I'll explain it:
I removed 12.75 inches from the center of the rack. You will see how I rejoined it right on one of the recesses.
I then cut 4 patches out of the remaining pieces to use on the inside. I glued the sections together as well as embedded galvanized wire from some fence to add some strength. I used the two part epoxy you'll see in the pictures I got from my local autobody supply house.
While the glue was a bit flexible I set it back down on the roof to make sure it formed well. I left it there overnight to dry.
I then sanded it down with 800 grit and applied a black bumper and trim polish (not pictured) in a shoe polish type applicator to bring the shine back.
To install I removed the headliner and drilled through the roof as the access cab does not have the factory installed weldbolts. The roof rack came with some caulking type washers that do a nice job of sealing it up but to be sure I siliconed all bolts again. I just came back from the car wash and no leaks.
Hopefully the pictures will answer any questions.