I replied on the PT forum as well check it out. Check out vibratesoftware.com tons of reading. I believe your pinion should be parallel to the crankshaft/trans angle under load. So if you trans angle is 3* down then your pinion should be 3* up. Also while doing those angles your driveshaft to pinion/trans angles should not be more than 3* and no less than 1/2* for the u joints to work properly.
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Dean
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