A lot of people just put them under the 60-40 back seat. (mine's full of towstraps and amps, but it fits) You could probably fab up something for the roof rack, but I wouldn't leave it there all the time.
Before I had my Con-Ferr rack I mounted mine on the factory rack. I built a clamp using two pieces of flat steel that clamped onto the factory crossbar. I then welded a flat bar straight up from that to bolt the jack to. I did that for both crossbars. You can also put it behind the rear seat in the cargo area diagonally(sp?) Just strap it down so if you roll it doesn't hit any passengers.
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