Dee Zee tool box with back rack questions

Hey, I just bought my first Toyota Tacoma (09, RWD) for a smoking hot deal last week. It came with a back rack (official back rack brand) already installed.
However, I am a carpenter and the crew cab is tight with all my tools in the back seat, so I bought a used Dee Zee tool box to store them in.

The problem is that the tool box is about 3/8" bigger than the L brackets coming from the back rack out onto the bed rails, so it doesn't fit nicely into the L shape.

I'm thinking about ripping a 2X4 down to 2 inches and bolting it into the back rack brackets, and screwing it through a piece of flatstock into the bed track (the one with the sliding hooks) on the other side. Then mounting my tool box on top.

But I'm worried about height, especially the height of the tool box in my rear windshield.

Another option would be to use an angle grinder and cut the back rack L brackets, but that might loosen the structural integrity of the rack. (and I need it to be strong.)

And that still doesn't solve the issue of how to mount the back end of the tool box to the sliding track or bed rails.
Anyone have any ideas for me?