Gearbox alignment is critical for a smooth and quiet running gearbox with long trouble-free service life.  If the gearbox is grossly misaligned, the driver (motor or engine) cannot transmit uniform rotation to the gearbox.  Consequently, the following problems may occur:
Vibration
Noisy running
Reduced bearing life
Premature gear tooth failure
The input shaft of the gearbox and the output shaft of the driver should be parallel, and the centerlines of both shafts should be in a common vertical plane.
Many different types and makes of driveshafts are being used.  The tolerances for the shaft angular misalignment vary.  Typically, a gearbox can tolerate larger misalignment than can a drive shaft. Rather, the tolerances should be obtained from the drive shaft suppliers.