Dave, I wouldn't give to much thought about be off a little. Look at the front suspension and how may joints there are that can move, then add in all the rear joints that move. Assuming every one of them was dead on tight, then you might worry about the 1/16" you are grinding out of the perch, but since we all know the spring pins and bushings are loose, whats a 1/16" really going to do?
Lots of folks drill new locating holes in the perches to center the tires in the fenders, most do it by eye and still get down the road OK.
Pinion angle changes with suspension movement, thats why you need to have full weight of empty truck on the axles. The pinion angle needs to stay in the working limits of the u-joint when full loaded or full extended.
