Here is a look at the brackets. I used 1.25 inch angle iron. The roof is not flat, so we had to angle the upright part of the bracket in slightly. It is an inexact science, and I used a grinder, a level, and soap stone to get the bottom angled somewhat correctly. Basically, I would put the upright on the angle iron on the factory rail and use the level to see how much to grind off the upright. I went little by little, and eventually got close.
Here is a look at the pedestal I put on top of the upright. This bracket is on the back of the roof rack. I would have done all 4 brackets like this, but my flooring dictated that I do something different on the front bracket. That being said I think the pedestal mount is the way to go.
This is what the rack itself looks like. It is a flat rack, and the bottom is some industrial shelving. The edge of the rack is 1.25 inch square tubing that I found in a dumpster. It was already bent at 90 in a square, so all I did was lengthen it and make it a little narrower. It is 86 inches x 41 inches.