Arcturus;
Observe relative position of UJ yokes when reassembling...UJ yoke of Driveshaft front section should be in-line with yoke of rear section front UJ, as a function of Spline Joint insertion (relative position can be adjusted to allow this by leaving gearbox in neutral such that Gearbox output shaft [and front Driveshaft section] can be easily turned, OR lifting rear tires from ground to allow turning Diff input Flange, OR some combination of both, to bring the Spline Joint into the preferred angular position).
Final assembled position should be as shown here at green.
Source:
http://www.sw-em.com/Driveshaft_and_U-Joint_Notes.htm
Note also that misalignment can be at angles other than 90 because of the multiple angles (teeth) spline joint can be inserted.
Good Hunting!