Power wagon pinion angles

So, I got this bad metal on metal rattling coming from the rear, I jacked up my truck and ran it up to speed and I get this really bad metal rattle sound. It happens on 1,2, and 3 at 16-2000 rpm, once I remove the drive shaft and run it up to speed, it's gone. Bad pinion angle? My transfer case is at 90* and my rear pinion angle is at -3*. I'm getting really frustrated here.
What do you mean it's at 90 degrees?!? The driveshaft angle?!?