I have a 96 800, that I race in 800 cc LTD class. For me there is a 2 part motor alignment, that is not in the manual.
I get my motor alignment be "close" to perfect, (which is rare, and why the shaft ends are curved, to allow for imperfections), and then there is fore and aft pump/prop/drive shaft (damper)play. Your pto boot and Carrier bearing/carbon seal is already off. I leave the rubber boot on the prop end on, since there is no play there,even though there a rubber damper there, the boot there is strong enough to prevent the compressing of the damper
I bolt on the pump with the drive shaft (and damper on), and the pto boot off. The motor has been aligned already. I then then loosen the 3 bracket bolts (13mm, slightly larger one at the front), and gently, slide the motor back till it just stops at the drive shaft damper, ( a second hand here helps to hold the shaft steady and not allow it move backwards).
Often I pull the drive shaft out on a motor and the damper is compressed, or in some cases squashed, or seemingly missing, and need a pick to get it out of the pto. The earlier skis have a soft spring in the cone, that forces the prop shaft forward against the thrust washer and the bearing. So there is some play at the thrust washer. When you hit the throttle, the pump draws the prop forward along with the drive shaft and that damper. The later models have a stronger spring, with little to no play. However it has been my experience that the spring is too strong and causes unnecessary binding. After I repair a prop, I like to be able to rotate the prop without cutting my finger. So, the bottom line to me, is that clacking on the trailer, is fine., it means the prop was installed without pinching/locking the thrust washer in the pump.