How should i go about creating a database the text book way?

Installed MYSQL, created an identical database structure to that of my current SQL database(windows - i use linux now) however it takes over 1 minute for my software to access the data, and thats on a blank database.

Is there any specific tables, or order in which tables / databases should be created, or perhaps perameters / variables that need to be amended or created?

An empty database should be accessed in less than a second. If you are getting long timeouts, it is almost definately because you are waiting on RDNS. Add entries to your /etc/hosts files for each machine, and this problem should vanish.

I get sub-1 second queries on databases up to 2 GiB in size if indexed properly.

Best,

Samuel