A quick set of links to help those moving from Word 2003 to Word 2007 or Word 2010, who have diagrams to convert to Smart Art.
Use this link for notes on converting to 2007 http://office.microsoft.com/en-us/word-help/use-word-2007-to-open-documents-created-in-previous-versions-of-word-HA010044475.aspx
Then follow this article for converting diagrams to Smart Art http://office.microsoft.com/en-au/word-help/diagram-conversion-HA010057149.aspx
Once the diagram is converted you should be able to apply custom animation or use the formatting available for Smart Art
Let me know how you go!