Oops forgot to log in for that last post.
I tried to use the standard mapping tool, but this has some limitations. So I ended up with the custom Xslt.
To create a map using a custom Xslt is relatively simple.
1. Create your Xslt file and extension Xml file and add to project.
2. Add a map to your project, specify the source and destination schema and click on the map grid.
3. You can now set the compiler properties, Custom Extension Xml and Custom Xsl Path
You now have a Biztalk Map that uses the custom Xslt.