Understood Dave. You will be fine. Grigg didn't say you are overthinking, I did. BTW: The loading, as it pertains to pinion angle, is referring to torque load/axle rotation during acceleration and braking and bumps. Not the load in the back of a pick up. Most of the chatter is about high HP cars and pounding thru the gears while accelerating as fast as possible. A Chevy motor is designed at 4 deg down at tranny with carb level. So your pinion yoke should be 4 up. (All things normal and stock).
As far as centering hole comment. Look at the assembly this way: The perch is flat up against the spring with pin in hole. Let's pretend perch is welded to spring. (you could actually clamp them) Then the perch radius rests on the tube. The tube/entire diff is free to rotate and slide while aligning and centering. You would have to really screw up the 1/16 radius modification to make a problem. The reworked radius does not have to be perfect. It may land on the tube and have a few gaps here and there. Call them weld gaps.
The truck is supposed to be at ride height when all this is done. I don't think the leaf springs on a 3/4T will move much with the bed on, and if they do, it won't rotate the axle. Up to you. So much easier to work on without. Get two 200 lb guys to stand on frame while tacking.
The off the shelf perch will have a hole right on the center line of radius. If your spring/truck is designed with spring pin to be on center of tube, you are good to go. Keep checking the WB to be near spec.