RE: Add a new company having the same master files and setup from the existing but empty transaction
There is no step by step guide available for this that will make sure you cover every table that is required in your setup.
That has to be evaluated case by case.
If you find the database information in your system you can get a list of all the tables in a specific company that holds data.
Then you need to include all the tables that are not transaction related.
The best approach would be to work together with your partner on this case so you make sure you do not miss out on some data that is important to have your system working.
If I got this request as a partner I would probably end up creating a copy of the company and then go in and delete all transaction related data instead of trying to move the setup. There are usually less transactional tables that needs to be handled than the number of setup tables that needs to be handled.
This is not a documented or supported approach but can be very efficient if it is performed by someone who knows the Dynamics NAV data structure well enough.