First off, we need to pin down exactly what equipment you are talking about.
I can't figure out what you mean by a "wwoden rudder spacing block"?
And a "shaft bushing" might be a prop shaft strut cutless bearing. If it is, the replacement of that item does not usually require a shaft/engine realignment.
If the through-hull packing gland or stuffing box is being called the "shaft bushing", the shaft "floats" in that housing to a small degree. Only a small amount of interference pressure from the packing would have a small influence on shaft support at this point.
When you align a shaft, you are making sure that the propellor shaft is in line with the gearbox output shaft. This is done by adjusting the engine mounts(and therefore the transmission), often wedges, and by checking the fitment and alignment of the gear box output shaft flange with the propellor shaft flange. If either the strut bearing or the stuffing box are messing up this alignment, something is drastically wrong.
Whenever an engine/shaft alignment is done, you need to make sure that there is no hog in the hull, the boat has been launched and in the water for at least a week, and that the shaft and strut are straight and in good condition.
1953 35' Commander "Adonis III"
1970 23' lancer project