The right way to do that is to have the engine and trans installed so that you can measure the angle of the transmission centerline. Then you can set the differential on the leaf springs, with the spring perches underneath, and rotate the pinion of the differential so that it is where you want it relative to the transmission centerline. Once you have that in position, tack the spring perches to the axle housing. For Cal-Tracs you should have about a 2 degree down angle on the pinion centerline, as compared to the transmission centerline. So, if the transmission is pointing down 2 degrees, the pinion angle should be level. This should also be done with the car at ride height, resting on the suspension. It's one of the last things I do when I'm setting up a rear end, because usually the car has to be mostly assembled to do it correctly.
As far as the axle housing ends, their position isn't that critical, I usually put them parallel to the pinion. If they are angled up or down a few degrees, no big deal.