The alignment tool keeps the pinion gear from falling too far into the prop shaft assembly tube. It helps seat the shims. Installing a 6' long pinion shaft is a challenge. What I have found that works is a 2x10 with a 3" hole in the center. Place the board on top of a 5 gallon bucket. Place the tube in this vertically then lower the shaft into the tube.
I have had to do this several times on occasion when the pinion bearing won't seat on the shims.