Joel,
Question – why do you need to create a war file and run in tomcat outside of ME?
I would recommend you to use deployment options – Exploded Archive for development mode and Packaged Archive for production mode.
If you are using packaged archive, it may take long to complete the re-export and drop it to your destination folder, considering your war file is 500 megs. Hence you are experiencing a slow export to war. We don’t have any tool inside MyEclipse IDE to generate an ant script for you. But you should be able to write your own ant script to generate the war file outside of ME. Sorry about that.