If anyone else is interested in finding out what i did.
I downloaded and installed the MYSQL migration agent, on the w2k3 server
i created and installed a new moodle server on my new squeaky clean linux box.
I only added the admin user on the moodle server. no other users.
I also installed the MySQL query browser and administrator onto the linux box
I gave the ip and user of the w2k3 machine access to the new mysql database.
I inputted my MSSQL and MYSQL server details, and I ran the migration program on the w2k3 server,
Whilst running it i had the opportunity of renaming the database moodle instead of moodle.dbo.
I then copied the moodledata folder from the w2k3 server to the linux box, and voila..
Granted i have simplified a few of the steps, and i did have to fiddle with a few ownership issues on a few files and folders, but i think a linux novice should be able to determine what to do.