At the top right of this very page there is a tab for "Tech Tips"
In there you'll find this very handy Tip for setting up drivelines.
http://www.stovebolt.com/techtips/driveline/setup/index.html

Some short answers: You want to do this with the complete truck, loaded as you'll likely drive it, bed on for sure. The pinion shaft should be parallel to the transmission output shaft.
Read the manuals, it's some cool stuff and I bet you have fun with this little project.

Grigg

•1951 GMC 250 in the Project Journals
•1948 Chevrolet 6400 - Detroit Diesel 4-53T - Roadranger 10 speed overdrive - 4 wheel disc brakes
•1952 Chevrolet 3800 pickup
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"First, get a clear notion of what you desire to accomplish, and then in all probability you will succeed in doing it..." -Henry Maudslay-