Cloning/duplication question...

I've had great success with this plug in so far and I'm going to be needing to duplicate to a new WPMU install. I realize that this plugin was built for duplication on one install, but is there any advice or tips anyone could share on how to duplicate from one install to another?

I know how to copy databases and import via myphpadmin, but that doesn't change all the links like this wonderful plugin does.

Any thoughts?

James