With what you have now vibration is likely. Driveshaft u joint angles should be equal but opposite. Or said simply, to alleviate vibration you should turn the pinion up (to zero) or figure out how to raise the tailshaft of the trans.

Is the car lowered? Bringing up rear ride height can help the angle between trans and driveshaft.

You are correct on wanting the pinion to point down as it will rotate up under load, how much depends on lots of variables though. But its not gonna happen without some vibration or other changes.