Guys, check me on this, but this really isn't that complicated... What you're really trying to measure is the net pinion angle relative to the trans output shaft. Forget about measuring on the driveshaft itself, there is some eccentricity as the joints turn over... Set the car flat on a drive-up lift, or get in an oil-change pit, so that the weight and suspension loading is "normal".
All measurements will be made on the flat of the trans output shaft and pinion input shaft flanges, and will be expressed in degrees from vertical. If the flange is tipped up, then it'll be a positive number, if perfectly vertical, it'll be "zero" degrees, and if tipped down, it'll be a negative number.
Step one: measure the angle of the trans output shaft flange. Most likely, it'll be around -3*, so tipped slightly downward. If the rear of the car is lowered more than the front, that angle will be slightly higher, but the absolute value is really unimportant, just the deviation from vertical.
Step two: measure the angle of the pinion input shaft flange the same way. Most likely, it'll be tipped slightly upwards, showing a positive number.
Step three: ADD the two numbers together. THIS is your net pinion angle. If there was no rear suspension, i.e. the rear was fixed, you'd want a ZERO pinion angle, with both flanges perfectly parallel to each other. However, since there IS a suspension for the rear axle, you'll want to "preload" the shaft slightly. When you step on the gas, the pinion will tend to rotate upwards, into a more positive angle, so you want to set the pinion angle slightly negative from parallel to compensate for the angular change. Since stick-shift cars tend to "launch" harder, you want an extra half-degree or so to compensate for that. If you have all rod-ends in the suspension, bushing deflection will be negligible, so you would reduce the amount of "preload" applied.
The whole idea is to distribute the joint angle (axis of the output or pinion shaft relative to the axis of the driveshaft itself) evenly between the two ends. The more angle there is, the more stress is applied to the joint, which is one of the reason that pickups with lift kits chew through U-joints faster than a stock-height truck. If the two shaft axes are parallel, then the angle is perfectly even at each end. Since maximum stress is delivered under acceleration, that's why we attempt to pre-load the angle slightly, so that under a hard launch, you GET a parallelism between the shaft axes.
Does all that make sense?