Engine alignment isn't difficult at all. But the alignment tool is important to have. As this alignment is critical to pump bearings, wear ring, driveshaft/PTO/impeller splines etc. Engine alignment is just a matter of installing the engine onto its mounts, loosely installing the 13mm bolts and barely lifting up the rear of the engine to slide a shim onto the mounting bolt between the top of the motor mount and the bottom of the bed pan of the engine. Then checking if the alignment rod slides directly into the PTO hole without hitting any area around that hole.
I purchased a shim kit from Watercraft Superstore(SBT). It comes with plenty of 0.5mm and 1mm shims to do the job correctly. I aligned both of my skis and this kit came in handy.