Hi,
The question of alignment of ship shaft line is more complex than an ordinary aggregate(for example el. motor and pump or fan).The procedure is not very common.
There is software for calculating all steps from design to mounting of the shaft.It exists one made by DNV (

[link Point to another website Only the registered members can access]
Nauticus Machinery

Nauticus Machinery - March 2008:
The new release contains updates and new features as described in the Release Document - March 2008.
Download Nauticus Machinery - March 2008 (823Mb) - link at the page
Release Document - March 2008). - link at the page

Unfortunately I haven't tried it.I suppose it need license to start and be used...
If you know if this can work properly or any other similar soft, please let me know.

Regards