Thanks both for the information.

I have decided to leave the primary constraints and unique constraints which by definition create indexes on the table creation statements so that the data is consistent. I will then insert the new data (these are scripts that insert into() select... from etc etc the five source databases) and afterwards re-build the indexes on all tables using the ALTER INDEX ALL ON statement.

I will then apply the non-clustered indexes for the foreign key fields and run sp_updatestats so that the Query optimizer work more effectively.

Does this seem like a good way of ensuring good performance from the indexes?

As a note, this will purely be a READ_ONLY database and therefore I have left the fillfactor at 100%