No, there should be no alignment required after lowering the cradle. Did you mark the driveshaft yokes prior to taking it out and put it back in the same exact position? I'm not saying that is the problem, but it could have something to do with it. The rubber "guibo" isolators are supposed to absorb driveshaft vibration, but it might be worth a shot trying to re-clock the driveshaft to one of the other of the three positions.
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