Hi Dave,
I tend to fit my prop shafts so that the inside end is above the waterline so that no water gets in that way.
Either the Kit or the plan should give motor/shaft size,length.
I drill a pilot hole through the hull then enlarge with drill and file so that the shaft will fit without any pressure to hold it in position.
Connect motor and shaft,align so that all are correct then fix shaft in position with 2 part Epoxy,I use the 5 minute type and have never had any problems.
I am better at doing it than typing!.
I hope this helps.
Len. 