I have had the clutch out of my bike 6 times, and have yet to use an alignment tool .
I measure the clutch disc outer edge with the pressure plates .
Try to get it even all the way around .
After you get the transmission into place, with the input shaft up against the clutch disc splines, rotate the output shaft of the transmission to move the input shaft, it will probably 'catch' the splines, but not go on .
With the clutch release rod installed in the transmission, give the release rod a good 'bump', to release the tension on the clutch disc and pressure plates, and the transmission should go on all the way .
May not work for someone else, but hasn't failed me yet !!