Moving websites between IIS servers is a breeze using iiscnfg.vbs script. I had to move existing IIS config as is to another machine, both Windows 2003 server machines. Destination server had nothing to merge. So import, export commands are:

1. iiscnfg /export /f C:\iiscnfg.xml /sp / /children
2. iiscnfg /import /f C:\iiscnfg.xml /sp / /dp / /children

Between both steps, all I had to do is find/replace IP address. Once import is done, changing IP address in DNS (which I maintain in zondedit) incrementally site by site made the transition simple and painless.

Check out Help Article on technet.