When you lift the front, you rotate the truck around the centerline of the rear wheel, + a minor weight transfer to the rear which will lower it an insignificant amount. This will not affect the angle of the pinion shaft with the tcase output shaft.

Optimally, you want the two shafts to be on the same axis. If you can't get that, you want them to be parallel and stay that way when the rear suspension cycles up/down.

On a leaf spring suspension, there's a flat plate on the axle (the perch) that's held flat on the spring pack with ubolts. A shim is like an acute wedge on a 1, 2, 3, etc. degree angle. If you want to tilt the pinion shaft down, you put the fat of the wedge to the rear, placed between the spring perch plate on the axle and the spring pack. This tilts the spring perch forward and the pinion down.

Using a longer rear shackle to lift the rear of a leafer tilts the pinion up as you lower only the rear end of the spring. To fix this, you use a shim installed as above. You can buy a cheap angle finder or a 'lectronic level with an angle display to check tcase output and pinion shaft angles to figure what kind of shim(s) you need.