Copied this out of the FAQ for you. In other words, the u joints should all have the same orientation.
Driveshaft Alignment. [Inquiry: I dropped the driveshaft to replace the center bearing and failed to mark the alignment. Now it vibrates. What do I do?] [Response: Dennis Hamblet:] The front section must be kept in the same alignment with the back section. The only approach I could suggest if yours appears out of whack is to remove the center bolts and rotate the rear shaft 1/4 turn then try it again. If it cures the vibrations you're home free, if not, rotate another 1/4 turn till you've tried all 4 combinations. [Response 2: Warner Bowles ] I believe that the yokes of the universals at the centre bearing have markings on them from manufacture which indicates the correct alignment. You will have to clean off the paint and any other build up which has accumulated on the yokes to see them. A second alternative is to ensure that the yokes on the universals at the centre bearing are parallel, (ie in the same plane). This will result in the universals working together rather acting against each other. If worse comes to worse you may be 180 degrees out but should still reduce the vibration. [Tom Irwin] Drive shafts are dynamically balanced, which is why some of the flange bolts are longer than the others. When removing, you should mark the position of each bolt too. [Response 3: John Yuristy ] Since you pulled the centre connecting spline apart, and there are about 17 teeth on there, you could have got it back together haphazardly in almost that many different orientations. Only one is right, and you can probably find it again by knowing how the yokes should be oriented w.r.t one another. If you did not take apart any U joints while you had it out, and therefore also possibly rotate the half-shafts in the process, then you get to try once or at most twice to get the original position. The vibes come from both the U joint yokes not operating with the right geometry, and also if you have lost the shaft mass balancing which was done originally.
So, orientation of U joint yokes should look like this if text can make an image.
[]-o]--------[]---[o-----------------o]-[]
1 2 3 4 5 6 7 8
where 1 is the front flange, 2 is U joint, 3 is front half shaft, 4 is centre bearing and spline, 5 is U joint, 6 is rear half shaft, 7 is U joint, 8 is rear flange.
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