When performing shaft alignment,  the most important goal is to align the machine to within proper tolerances.

One criterion that has an impact on the tolerances that should be used is identifying and selecting the correct coupling type. In the setup shown below in Figure 1, spacer coupling tolerances were being used. However, in order to achieve a proper alignment, the alignment should have been performed using short flex tolerances.

Between the two shafts, a long coupling is used to connect them, however, the connection between the motor shaft and the spacer (left side in the picture) is rigidly coupled and has no flexible element. Thus this setup should be treated as a continuous extension of the motor shaft. Therefore, the alignment should be performed using the short flex tolerances at the flexible coupling on the right side. Spacer tolerances should only be used when the distance between the two flex planes of coupling is four inches or greater.
Rigid Coupling

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by Tim Rogers CRL