The driveshaft will have a flange at the rear which allows some articular in 2 dimensions (or should). Order the correct length and then make your mounts with the driveshaft in place keeping I mind the drivetrain angles. Independent rear suspension is just that; the rear suspension moves independently of the chassis. This also goes for the diff. However, the diff sees a small amount of deflection during acceleration so although fully independent, it does not operate fully independent.
The only other way to measure pinion height is relative to the ground. However, unless you have a specific alignment table with a perfectly flat ground, your results will be skewed.
Its all relative in terms of the driveshaft. Read some more on the spicer link I provided on how they go about determining driveshaft angles.
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