The trans to driveshaft angle really isn't taken into consideration when your trying to get your driveshaft/pinion angle. The angle that's important is the angle of the pinion relative to the engine/trans angle. If you engine/trans angle is "down" 3 degrees then your pinion should be set so that it's pointed up 3 degrees when the pinion is under load (under acceleration). Your goal is to get the pinion to be parallel to the drive line when your accelerating.
In the end, the angle of the driveshaft with respect to the trans doesn't really matter unless you have a 4 wheel drive and it's jacked up so high that the driveshaft u-joints are binding.
treblig