Hello,

As all of the domains are on the same server, you need to create separate Nginx server blocks for each sub domain. You can follow the steps on how to do that here:

https://www.digitalocean.com/community/tutorials/how-to-set-up-nginx-server-blocks-virtual-hosts-on-ubuntu-16-04

After that you need to make sure that you create a separate database and database user for each website.

Once you have these two things, you can move the data of your website as you described in your post. Even a migration plugin should work in this case.

Hope that this helps!
Regards,
Bobby