Hi Aaron:
If you have a big dataset, using MySQL Query Browser is definitely not the way to go. You can use the Migration Wizard included in MySQL Workbench. Make sure you get a recent version (recent = latest) since the Migration Wizard was released about two moths ago. You can download it from here:
http://www.mysql.com/downloads/workbench/
You can use this blog post to get an idea about the process: "How-To: Guide to Database Migration from Microsoft SQL Server using MySQL Workbench" at
http://mysqlworkbench.org/?p=1350
Take into account that that post is about MS SQL Server to MySQL migration, so you would have to select your MySQL instance in your WIN2003 server as your source instead of a MSSQL one. Run the full migration, just make sure to uncheck the "Create schema in target RDBMS" checkbox in the Target Creation Options page. This way you will not override your existent schema so you can move to the data copying part, that is the one that you really want.
The data copy is done by directly querying your source DB using MySQL's connector C by a multithreaded independent app running in the backend, so it should be pretty efficient. But beware that it can take some time to finish depending on the size of your data and the bandwith of the network links between the machine that has Workbench running and your servers.
Please report back how it went and good luck.
Sergio A. de la Cruz RodrÃguez
Software Developer
Oracle Corp.