In what file does SQL Server Store the configuration data? Where does SQL Server 2014 store the configuration data? Such as the certificate references for SSL and the size limits and allocations?
Basically there is not a single place where ever configuration can be found.  

The more generally used configurations can be found here Server Configuration Options. But they do not necessarily cover everything that you might want to configure.

For example:  Enable SSL Encryption for SQL Server using Microsoft Management Console

Also you can find some information on size limits and allocations at: Features Supported by the Editions of SQL Server 2014

Perhaps these examples will get you started.