It does all need to be done, but the estimate seems a little high if it was a plain R&R kind of
repair.
If the shaft is scored or not true it may need replacing at about $350, alignment is normally included with the stuffing box/shaft
repairs. However if the misalignment is caused by broken motor mounts that's an expensive
repair.
Shaft zincs are a $20 item normally, your gonna need more detail on what he intends to replace/repair.
I just looked at some records and in 2006 I had a 27' boat hauled, painted, relauched and all the
repairs mentioned (and a little more) for $1900 by my yard. Shaft was in good shape, cutlass bearing was only part replaced.
BTW I've seen boats that have been "aligned" using wooden wedges, etc. where motor mounts are shot, you really need to take a good look at what things look like.